I think zza1pqx is right. PunkBuster or not, if you join somsone running the same mod, i don't think anything bad will happen. The only reason i can think of you getting banned for, is
joining a ofiicial Nova sherver while running your mod. Just make sure you click on your normal shortcut before joining a nova server
Although, i understand your concern chief, banning is a terrible thing
BTW, i think you have to join a server before any banning can be done. I don't think logging in with your mod would get you banned