Typing `./configure` wont work but something like `./configure CFLAGS="-Wno-error=implicit-function-declaration"` (or whatever flag) might work (IIRC it is possible to pass flags to the compiler invocations used for checking out the existence of features) without needing to recreate it.

Also chances are you can shove that flag in some old `configure.in` and have it work with an old autoconf for years before it having to update it :-P.