I think it's a great idea, as long as you can fit the controls you want on your new control panel.
Personally, I don't think there was that much distinctive about the Moon Patrol cabinet that losing it to a MAME cab would have been that much of a loss. Still, I do think it's great that you are making the effort not to damage anything.
I did "chop" off part of the front of my Roadblasters cab to fit a SlikStik, so I'm guilty of MAME-ifying a cab. Of course, it was a stripped cab, with no sideart, boards, CP, bezel, or marquee. Basically a big wood box.
Do I sound like I'm rationalizing?

Kevin