Stevie, I'm interpreting that you're looking at two choices:
1. Everyone wears headphones and goes direct, or
2. Everyone wears headphones and only the guitar amps (and drums) aren't direct.
Griff's idea is good. For me, I'd lean toward your thought of recording them direct - just because everyone is wearing headphones anyway, and as you said the amps aren't an integral part of the guitarists' sound.
Another option if they don't like going direct is to put the amps out in a hall or in another room and mic them there. Barring that, stick them in the corner of your L shape and/or use gobo panels or something similar to wall them off. You'd get a little room volume but that might make it more manageable.
"Of all the world's bassists, I'm one of them!" - Lug