Is there any general solution to the linear differential system?
$i\begin{pmatrix}\dot{c_1}(t) \\ \ \dot{c_2}(t) \\ \ \dot{c_3}(t) \end{pmatrix} = \begin{pmatrix} e_1 & J & J\\ J & e_2 & J \\ J & J & e_3 \\ \end{pmatrix} \begin{pmatrix} c_1(t) \\ c_2(t) \\ c_3(t) \end{pmatrix} $.
I can find the eigenvalues when $e_1=e_2$ (or in general when two values of the diagonal terms are the same, but I cannot find a way to find the solution to the general system, as I cannot find the eigenvalues with analytical techniques.
The initial conditions are $c_1(0)=1,c_2(0)=c_3(0)=0$.
Is there a way to solve it? Or at least in the regime $e_2=-e_3$?
Let $A$ be your $3\times 3$ matrix. You ask for the first column of $e^{-itA}$ in a formal form; of course, it's practically impossible as shown by @Kyle (I wonder how long the calculation lasted!). That shows, on the one hand,the extraordinary power of the formal calculus and, on the other hand, its uselessness in this extreme case.
Note that the eigenvalues of $e^{-itA}$ are in the form $(e^{-it\lambda_j})_j$ where $\lambda_j\in\mathbb{R}$; then your $(c_j(t))$ are linear combinations of many $\sin(),\cos()$ and there is not any dominant term when $t\rightarrow\infty$. Thus the solution is a tangle of oscillating terms and, indeed, it's difficult to have an idea about the behavior of the solutions; in conclusion, it's a difficult problem and that's why one asks students to work on the subject; otherwise you would be useless.
Special cases happen when $\lambda_j/\lambda_k$ is closed to a rational number $p/q$ with not too large $p,q$.