I'm using the definitions/conventions of $C^*$-algebras and their representations from Conway's Functional Analysis (VIII.5). If I need to supplement any definition, let me know.
Let $X$ be a compact Hausdorff space. Let $\mu$ be a positive Borel measure on $X$. Then $$ \pi_\mu:C(X)\to \mathscr B(L^2(X,\mu)),\phi\mapsto(f\mapsto \phi\cdot f) $$ defines a representation. I've shown that this representation is cyclic. I've also shown that if $\nu$ is another positive Borel measure on $X$, then $\mu\perp\nu$ implies that $\pi_\mu\oplus\pi_\nu\cong \pi_{\mu+\nu}$, which is cyclic.
I want to show that it goes the other way around too: if $\pi_\mu\oplus\pi_v\cong\pi_{\tau}$ where $\tau$ is a pos. Borel measure on $X$, then $\mu\perp\nu$.
Attempt 1:
Say $\pi_\mu\oplus\pi_n$ is cyclic with cyclic vector $(e,f)$. Arguing by contradiction, if $\pi\not\perp\mu$, then we should be able to find $(g_1,g_2)\in L^2(X,\mu)\oplus L^2(X,\nu)$ such that no net of the form $(\phi_i e,\phi_i f)$ converges to $(g_1,g_2)$. Problem is that $\mu$ and $\nu$ not being mutually singular doesn't yield the existence of an interesting set, rather it says that no interesting set exists (namely, no $A\subset X$ such that $\mu(A)=0,\nu(X-A)=0$), so I don't think I could argue here with indicator functions or something.
Attempt 2:
Since $\pi_\mu\oplus\pi_\nu$ is cyclic with cyclic vector $(e,f)$, it corresponds to the positive linear functional $f$ on $C(X)$ defined by $$ f:\phi\mapsto \langle \phi f,f\rangle+\langle \phi g,g\rangle=\int \phi f\overline f d\mu+\int \phi g\overline g d\nu. $$ By Riesz representation this functional corresponds to a positive Radon measure $\tau$: $$ f(\phi)=\int \phi d\tau. $$ If $\mu$ and $\nu$ are Radon (which I think is a fair assumption), then I believe this implies that $f\overline f \mu+g\overline g\nu=\tau$. Does this yield something interesting?
Attempt 3:
I know that any cyclic representation on $C(X)$ is of the form $\pi_\tau$ for some Radon measure $\tau$. Thus if we write $\pi_\mu\oplus\pi_\nu\cong \pi_\tau$, and we argue by contradiction, I would hope to show that the isomorphism $\Phi$ from $\pi_\tau$ to $\pi_\mu\oplus \pi_\nu$ is the same as for the case where $\mu\perp\nu$, namely $$ f\mapsto (f,f) $$ which I can then show is not surjective. If $\tau$ is a finite measure, then the constant functions are $\tau$-integrable, and since $\Phi$ is a morphism between representations, we would get $$ \Phi(f)=\Phi(f\cdot 1)=f\cdot\Phi(1) $$ for any continuous $f$. Since $\Phi=(\Phi_1,\Phi_2)$ is surjective, this shows that $\Phi_1(1)\neq 0 $ a.e. [$\mu$] and $\Phi_2(1)\neq 0$ a.e. [$\nu$], hence $\Phi_i(1)$ are cyclic vectors. Since $\tau$ is a Radon measure, $C(X)$ lies dense in $L^ 2(\tau)$ by Lusin's Theorem. This could potentially be useful?
I will write $H_{\tau} := L^2(X,\tau)$ and denote the representation of $C(X)$ on $L^2(X,\tau)$ by multiplication operators by $\pi_{\tau}$ whenever $\tau$ is a Borel measure on $X$. I assume you know that each $\pi_{\tau}$ is a cyclic representation of $C(X)$ and that any cyclic representation of $C(X)$ is unitarily equivalent to some $\pi_{\tau}$ (the form of your question suggests this). To focus on the core ideas I sketch details only in "footnotes." The conceptual key is that if $\mu$ and $\nu$ are not mutually singular, there is a nonzero measure $\sigma$ with $\sigma \ll \mu$ and $\sigma \ll \nu$.1
One approach is by analyzing commutants. In general, $\tau$ is any measure and $\tau' \ll \tau$, the $L^2$ space $H_{\tau}$ contains a subspace isomorphic to $H_{\tau'}$,2 such that an isometry implementing this isomorphism also implements a unitary equivalence between $\pi_{\tau'}$ and a subrepresentation of $\pi_{\tau}$.3 So if $\mu$ and $\nu$ are not mutually singular, there is thus a nonzero $\sigma$ such that $\pi := \pi_{\mu} \oplus \pi_{\nu}$ contains a subrepresentation unitarily equivalent to $\pi_{\sigma} \oplus \pi_{\sigma}$,4 and it suffices to show that $\pi_{\sigma} \oplus \pi_{\sigma}$ is not cyclic.5 But the commutant of any cyclic representation of $C(X)$ is abelian6 while the commutant of $\pi(C(X))$ in $\mathcal{B}(H_{\sigma} \oplus H_{\sigma})$ clearly is not.7 End of proof.
Some language from representation theory is helpful here. A representation $\tau$ of a $C^*$-algebra is said to be "multiplicity-free" if it contains no subrepresentation unitarily equivalent to a representation of the form $\tau' \oplus \tau'$, where $\tau'$ is a nonzero representation. While the representations $\pi_{\tau}$ of $C(X)$ are all multiplicity-free8, the argument above shows that when $\mu$ and $\nu$ are not mutually singular, the $\pi_{\mu} \oplus \pi_{\nu}$ is not multiplicity-free. (I am not sure if this perspective or language appears in Conway, but see e.g. Arveson's Invitation to $C^*$-algebras for more from this perspective.)
As an alternative to analyzing commutants, one can also simply exhibit nonzero vectors in the orthocomplements of the spaces $\pi(C(X)) \xi$ when the measures $\mu$ and $\nu$ are not mutually singular. As before, we will use the existence of a nonzero measure $\sigma$ with $\sigma \ll \mu$ and $\sigma \ll \nu$.
For motivation, consider the example of $X$ finite and discrete, with $\mu$ and $\nu$ counting measures on subsets $E$ and $F$ of $X$ respectively9; such representations $\mu$ and $\nu$ are plainly mutually singular iff $E$ and $F$ are disjoint. By indexing the elements of $E$ and $F$, one can identify $H_{\mu}$ with $\mathbb{C}^{|E|}$ and $H_{\nu}$ with $\mathbb{C}^{|F|}$ and the action of $\pi$ on $H := \mathbb{C}^{|E|+|F|}$ is by diagonal matrices, where the diagonal entries of $f \in C(X)$ list the values of $f$ first on $E$ and then on $F$. If $E$ and $F$ are disjoint (i.e., if $\mu$ and $\nu$ are mutually singular), the image of $\pi$ is easily seen to be the set of all diagonal matrices, and as you already know, this representation is cyclic.10 If $E$ and $F$ are not disjoint (i.e., if $\mu$ and $\nu$ fail to be mutually singular), equally clear is that the the image of $\pi$ is not the set of all diagonal matrices, but a subspace of diagonal matrices having some fixed pair of entries equal to one another.11 Fixing indices $1 \leq m \leq |E| < n \leq |E| + |F|$ with the property that the $m$th and $n$th diagonal entries of each matrix $\pi(f)$ are equal, let $\xi \in H$ be given. If $\xi_m$ (resp. $\xi_n$ ) happens to be zero, then the $m$th standard basis vector $e_m$ (resp. the $n$th standard basis vector $e_n$) is nonzero and in $[\pi(C(X))\xi]^{\perp}$,12 while if both $\xi_m$ and $\xi_n$ are nonzero, then the nonzero vector $\bar{\xi_m}^{-1} e_m - \bar{\xi_n}^{-1} e_n$ is in $[\pi(C(X))\xi]^{\perp}$.13 So we can see very concretely how $\pi$ fails to be cyclic when $E$ and $F$ are not mutually singular in this case.
With some care, the approach just outlined extends to the general case. Fix a nonzero $\sigma$ with $\sigma \ll \mu$ and $\sigma \ll \nu$ and let $h_{\sigma,\mu}$ and $h_{\sigma,\nu}$ respectively denote the Radon-Nikodym derivatives of $\sigma$ with respect to $\mu$ and $\nu$, and let $\xi = (\xi_1, \xi_2) \in H := H_{\mu} \oplus H_{\nu}$ be given. If $\xi_1$ (resp. $\xi_2$) vanishes on a set of positive $\sigma$-measure, $\xi_1$ (resp. $\xi_2$) then also vanishes on a set of positive measure $P$ for which $1_P h_{\sigma,\mu}$ is in $L^2(\mu)$, and the vector $(1_P h_{\sigma,\mu},0)$ (resp. $(0,1_P h_{\sigma,\nu})$) is then seen to be a nonzero vector in $[\pi(C(X)) \xi]^{\perp}$.14 Similarly, if both $\xi_1$ and $\xi_2$ are nonzero almost everywhere, there is $c > 0$ for which the set $\{x \in X: \text{$|\xi_1| \geq c$ and $|\xi_2| \geq c$}\}$ has positive $\sigma$-measure, and a subset $P$ of this set, also of positive $\sigma$-measure, for which $(1_P \bar{\xi_1}^{-1} h_{\sigma,\mu}, -1_P \bar{\xi_2}^{-1} h_{\sigma,\nu})$ is in $H$, where it is seen to be a nonzero vector15 in $[\pi(C(X)) \xi]^{\perp}$.16