You could implement a 68K to 68K compiler that treats Petunia as the target architecture, replacing all legacy hardware code with calls into the core E-UAE emulator. The performance hit still sounds atrocious, though. What types of applications would benefit from this that don't already benefit from Petunia?
Re: GPL, I don't see any conflicts. Petunia is an operating system service, just like file I/O and memory allocation.