I'd have no problem of allowing someone to use a different skill for magic, as long as a few basic rules are followed:
- there must be 3 different skills, don't roll everything into 1.
- it must make sense for the character concept. A kung-fu monk with fists-style magic? No Problem. Fists for magic, just because fists is a fighting skill in it's own right? Come on, you can do better than that.
- Specialization through refinement still applies, but no other benefits for the purpose of spellcasting. Yes, speed powers add to athletics rolls. No, it does not add to magic rolls, even if you use athletics for it. That's what refinement is for. The same goes for strength powers, you don't add strength stress bonus to a fists spell, that's just not how it works.
I wouldn't even charge refresh for it, since it could just be a different power with a different set of skills that just does the same as evocation and thaumaturgy.