Recompiling source code will be fine - you 'just' require the source. However, some instructions behave differently, so without code analysis you will never know if the code at hand works OK.
If you recompile the code for ColdFire, you could put a ColdFire identifier for the code in the executable. This is how PPC code in an Amiga executable works. There is probably already a ColdFire ELF code identifier if using AROS. Vbbc/vasm may already be able to compile and assemble it. I have assembled ColdFire code on my Amiga into an executable with vasm. I disassembled which verified that it did use the ColdFire instructions.