I admit I haven't been keeping up with this, so I apologise if it's been addressed; but there's one glaring thing about why Atlas isn't a terrorist missing from the OP which stands out like an iceberg at a Titanic convention:
"Because I don't want to be."
"Because I don't want to be."
At the age of five, Skagra decided emphatically that God did not exist. This revelation tends to make most people in the universe who have it react in one of two ways - with relief or with despair. Only Skagra responded to it by thinking, 'Wait a second. That means there's a situation vacant.'