A patch to re-do Vala support would be a larger patch at this stage, though overall it would certainly streamline Vala support in automake.
Also, being frank, removing "Vala-generated-C" support is the only way I would offer to have anything to do with making such a patch, as (as far as I can see) that route would be much simpler than retaining the current support (even in deprecated form) while also putting in "normal" Vala compiler support.
I also sympathise with the maintainers if they would rather not simply remove the existing C-from-Vala support. I would offer the following observation, though: as far as I can tell, most Vala developers are migrating away from autotools (if they used it) to meson, along with the rest of the GNOME ecosystem. Also, it's fairly straightforward to get old versions of automake where needed. This could be used to argue in either direction: on the one hand, replacing the current Vala support with "normal" support would annoy a small proportion (committed automake users) of a small user group (Vala programmers). On the other, it would benefit few users.
It might be best then to make the decision based on automake's other users? I for one would not be terribly happy as an automake maintainer at having to keep Vala support working long-term, and to be honest, the patch I have submitted, while fixing bugs in Vala support, will slightly add to the maintenance burden.
My own use case is that I've rewritten GNU Zile (a small Emacs clone) in Vala. Users building it will have to install glib anyway, and so while it feels nice that they don't need a Vala compiler, as I said before, I don't think in practice it's a big deal (even for a Zile user who doesn't care about Vala, they're likely to be able to install valac easily using whatever package manager they have).