why would mario be able to use goombas?
If this was some sort of arranged arena battle and mario had access to mushrooms, fire flowers, etc. then I'd go with mario. You can't just shoot a gun and expect to hit mario. He's been dodging sentient bullets for years.
But if the fight took place in some sort of vietnam jungle type conflict where mario had gone awol and started his own tribe/cult deep in country where mushroom retainers were putting koopa heads on spikes and dancing around naked covered in blood then I'd have faith that snake could sneak in and kill mario...but maybe mario would be so far gone at that point that he'd actually want Snake to take him out...and then Snake would raise the head of mario out over the the rogue tribe ending the madness...
Super Mario World 3! Koopocalypse Now!