Instersting idea. I absolutely love how MMBN sounds. Basically it uses a lot of squarewaves, made with the original GBC channels, added with some simple chords or percussions made with the GBA channels.
The good news is that you'd have to only rip the simple chords and percussions from the game with a program named GBA2MID, and you can get them easily from the game.
The bad news is that perfect square waves are hard to reproduce in SF2, because of interpolation. Most/All soundfont-midi compatible drivers will use interpolation and deteriorate significantly the sharp edges of a square wave. Also, the Square Waves from the GBA are not exactly pure square waves but are bandpass-filtered. I'm pretty sure the difference is noticeable by hear. If you only use one square wave sample, the filtering will "translate" as you will go to different tonality, and add the interpolation problem to that and you get some very inaccurate sound.
So your best bet would be to actually "record" the square waves from a real GBA or from an emulator (I'm not sure how well the bandpass filtering is emulated), and do it for regular pitch intervals (for example every 5th). You can be pretty sure that the translation of the filtering and the interpolation will not be noticeable by hear for pitches close enough to the original.
So with some decent set of squarewave samples, I'm pretty sure it's possible to get accurate gameboy-like sound in a soundfont, it's just not that easy. Also you'd have to do that will all the 3 possible duty cycles, and maybe some different waveforms that can be used by Gameboy channel 3 (but I'm pretty sure only square is used in MMBN games).