It was hero VS hero in appearance only with regards to SI. We all knew that we were dealing with Skrulls, so each and every hero was to be suspected as a potential Skrull. Yes, heroes were corrupted by the hammers in FI, but the 'big bad' was the Serpent, and the main focus of the event was most certainly the threat he and his army presented world wide. Remember when Grey Gargoyle turned to stone all of Paris? I'd wager that was pretty bad. The Sentry, who I consider a villain (though I suppose there are those will argue the point), ripped Ares in half, destroyed Asgard, and if not for Loki probably would have done plenty more damage. Red Skull took Captain America off the map for a long while after he "killed" him. Bastion murdered Nightcrawler. I mean, there are plenty of examples of acts taken by villains that are extremely heinous and rival the examples you've given, but I think the added bit that it was heroes who did the things you continue to bring up make them seem worse.