I am working on a fork from the v0.5 sources to add cheat and debugger functionality, similar to what I did with FCE Ultra (forked to FCEUd)
Watch the gscentral.org forums for more info.
You should consider submitting your cheating code back to Hacktarux for inclusion in the official releases, since this is something a lot of people would want.
Maybe bumping an old thread...is there any progress yet? Choosing a different program for cheating is not possible because Mupen64 is the only viable alternative for Linux N64 emulation. The forums linked in this thread do not contain information about this mod.