I'd apply the penalties to your original affiliation instead of the new one to determine your benefits while undercover. Can't be seen as having too close a connection to your real friends, right?
Hey, Sirp, why do some affiliations have +2 score for being in at least one of several classes, while others have +1 for each class? I don't care which way you go, but it should be consistent, I think.
Also, there are still several affiliations whose benefits need revising (though you may have done so since I last remember checking). I'll bug you about it later if I remember.