Well, honestly, I think that the whole "evil mushroom" thing was just something the English localization team came up with for their instruction manual to SMB. Notice how they're rarely referred to as that in any recent game. And take the Goombas' real name: Kuribo, which is a pun on the Japanese word for "chestnut" (similar to Kuririn or Kuriza from Dragon Ball), and you might start to realize where these people were going with this.