Kirsten,
The only redeeming aspect I see to extra credit is that it should be called "extra activity", in that it allows a student to showcase their talents in way that's unique to them. But most classes already have a category for that, called "projects". As you state, and I agree, EC usually monkeys with points and grades and less with learning. For me, I just choose not to offer it. Other opinions may vary, and that's OK too.
Barry Westling