Maybe I missed something, but how much overlap are we talking about? A few mm, or like inches?

Almost any road frame short of a mega-slack touring frame is going to have a little bit of overlap (heck, I have a road frame with a 50mm rake fork in it and it still has a tiny bit of overlap with clipless pedals), and stuff like shorter cranks and smaller clips isn't going to buy you much more than 1/2" or so.

She needs to ride freewheel until she's comfortable with the bike overall, at which point overlap won't be a problem. And she can ride freewheel, because you didn't put your girlfriend who isn't experienced enough to deal with overlap on a brakeless fixed gear. Or do we need to go get the Stupid Helmet?