Suppose we have a separable, irreducible quartic that has 4 complex roots, and so it has 2 complex conjugate pairs. Does this then mean that the Galois group of this polynomial over the rationals cannot contain a 3-cycle, since this would not preserve the property that each of these roots have a complex conjugate pair?
I am confused about what properties are preserved by the galois group.
Let us view the Galois group $G$ as a group of permutations on the four roots.
No, the fact that the roots form two complex conjugate pairs does NOT let us conclude that the group has no elements of order three (I will produce an example if necessary). All it implies is that the group $G$ contains a product of two disjoint 2-cycles.
What is confusing you is probably the fact that the complex conjugation does not necessarily belong to the center of $G$. In other words, there may be automorphisms $\tau$ that don't commute with complex conjugation. For such an automorphism $\overline{\tau(z)}$ may be different from $\tau(\overline{z}).$