I think it's probably very confronting for her to take on clipless pedals and cyclocross riding all at once. You may need to back off a little and let her get confident with one or the other first.
I went to clipless pedals on the roadie more years ago than I would like to count after doing some silly things in toeclips that had fibreglass straps and wouldn't release me. A couple of good gumby stacks there! I then rode my clipless pedals on the road for years and would never ride with anything else.
Fast-forwarding to late last year, my DH got the mountain bike bug and I decided to join him. The bike I bought came with clipless pedals and I was faced with a dilemma. The concept of riding on loose surfaces scared me spitless (probably a bit like your GF changing to cyclocross) and I didn't want to have clipless pedals in case I couldn't get out in time when I came to a grinding halt on an obstacle I couldn't manage etc. But I also already knew the joy of clipless and felt really insecure without my feet clipped in.
In the end I left the clipless pedals on the bike and used the little plastic platform insert they give you to try the bike in the shop for a couple of rides until I got more comfy. Then I bit the bullet, clipped in and fell off enough times to remove the bark from both elbows and both knees! I'd never go back to platforms now.
I have since been responsible for corrupting many of my friends to clipless off-road and none of them would go back either. I think the main thing here is to be patient. If you want her to ride cyclocross you need to let her do it on her terms - perhaps that means sans clipless for a while. Then clipless can be the big improvement for her when she gets more confident with the whole not-so-smooth surface thing? Either that, or get her riding clipless on the smooth smooth road first?