The problem of whether two maps define the same homomorphism is insoluble in general. Any (centreless) group $G$ with insoluble word problem gives a counter-example.
Note that the problem is always soluble for finite groups, and for finitely generated abelian groups, by brute-force methods. So this doesn't answer what you actually want to know. But it does answer the question as it is posed...
I will explain why such groups give counter-examples, but first I will explain what the word problem is.
Let $G$ be a group. Then if $\mathcal{P}=\langle X; \mathbf{r}\rangle$ is a presentation for $G$ (and we shall assume both $X$ and $\mathbf{r}$ are finite, but this isn't necessary (what you really need is "recursive")) then $\mathcal{P}$ has insoluble word problem if it is undecidable whether a word $w(X)=_{\mathcal{P}}1$ or not. This is invariant of the presentation, and so we can talk about the word problem for the group defined by $\mathcal{P}$, which is $G$ here.
Right, so, we have a group $G$ which has insoluble word problem. Now, $G$ embeds into $\operatorname{Aut}(G)$ because $G$ is centreless. Thus, $\operatorname{Aut}(G)$ has insoluble word problem (if a group has soluble word problem then so does all its subgroups, so reverse this to get what I just wrote). That is, if $G=\langle a, \ldots, c\rangle$ then it is undecidable whether the map $\phi: a\mapsto A, \ldots, c\mapsto C$ is the trivial automorphism or not. Therefore, we are done.
Two comments: Firstly, I think that the result should hold for all $G$ with insoluble word problem, not just those with trivial centre. Secondly, I would be interested to know if someone can come up with a similar counter-example for when the homomorphisms are proper. Does this just follow from groups where the subgroup membership problem is insoluble? (One can assume the subgroup in question is normal, e.g. for $g\in F_2\times F_2$ it is undecidable whether $g$ is in the kernel of the map $F_2\times F_2\rightarrow F_2\rightarrow H$ where $H$ has insoluble word problem.)