(I think, I do not understand your question in its entirety, because I don't know how to take a pushout of objects of two _different_ categories)
If you want to compute $H_*(X,A)$, you actually should take the complex $C_*(X,A):=C_*(\tilde{X},\mathbb Z) \times_{\pi_1(X)} A$.
In general, for an arbitrary $\pi_1(X)$-module the homology groups $H_*(X,A)$ do not equal the homology of some topological space, because $H_0(X,A)$ does not necessary equal $\mathbb Z$ even if $X$ is path-connected.