My theory on the whole "betrayed the Mushroom Kingdom" thing is that Goombas were with the Mushroom Kingdom in the first place (like Goomba Village in PM) until Bowser came along, and the Goombas simply defected to the stronger side.
Spoiler Below Evidence for that theory is in SPM, when you first play as Luigi in Castle Bleck. Two Goombas are there to help you, but when they get caught, the Goombas immediately defected from Bowser's army over to Count Bleck. Then again, the Goombas in Bowser's Inside Story do seem to be die-hard devotees of Bowser, but maybe that's 'cause they were in a cage. Besides, those three minions (the ones that helped out with the whole Banzai Bill thing) also betrayed Bowser, throwing him into a safe and all.