Has O'Neill ever been portrayed as evil?
From a certain point of view, every other member of SG-1 has "turned" evil at some point.
Teal'c got brainwashed by Apophis and joined his ranks again.
Daniel was under influence of the sarcophagus, and in Harsesis's vision he was literally a villain.
Regarding Sam, you could count the replicator Sam as an evil version of her. Also, in the episode Nightwalkers, she was pretending to be under Goa'uld influence and acted so.
I'm sure there's more examples that I can't remember now from the top of my head.
What about O'Neill? Was he ever portrayed as a villain?