Like I said, he absolutely sympathizes with them. He still points nukes at Legion territory though, so he's clearly not loyal.
[linkAFAIK, the NCR causes problems (For reasons I don't recall; the methods, I do, but the reasons seemed to be pretty spurious at best), the Courier's just there. You didn't cause anything... except in Ulysses' ridiculously weird Great Person view.To be fair, you did cause Ulysses some problems. *cough cough*divide*cough*nuclearexplosionseverywhere*cou gh*