sudomod

I'm new to most of this stuff so please don't get mad if I use the wrong terminology. What would be the best way to use the buttons from a gameboy dmg to use with the pi zero without using the original gameboy motherboard.

I would think your best bet is a third party pcb. There are quite a few options out there, such as here on Pocket Adventure's site.
http://www.pocketadventures.com/products.asp