Sure the NID and the SGC are enemies, but the NID are not necessarily evil. They're an oversight group that's supposed to catch super-secret government groups before they go overboard. The problem with the SGC is that they routinely have to go overboard in order to save the world.
Vathara wrote a wonderful fic sometime back: Hearts on Barbed Wire http://www.fanfiction.net/s/2013341/1/Hearts_on_Barbed_Wire It points out that, yes, the SGC are good guys; yes, they save the world, but unfortunately, yes, they are committing treason. They are running a private war without the knowledge of the people. The President is committing treason by ordering them to do so, they are committing treason by following those orders. There are checks and balances in place for a reason. Actually, it's part of a series, Urban Legends, which is really fabulous in a whole variety of ways and which I definitely recommend.
Re: Oh I do wish you would write this one
Vathara wrote a wonderful fic sometime back: Hearts on Barbed Wire
http://www.fanfiction.net/s/2013341/1/Hearts_on_Barbed_Wire
It points out that, yes, the SGC are good guys; yes, they save the world, but unfortunately, yes, they are committing treason. They are running a private war without the knowledge of the people. The President is committing treason by ordering them to do so, they are committing treason by following those orders. There are checks and balances in place for a reason.
Actually, it's part of a series, Urban Legends, which is really fabulous in a whole variety of ways and which I definitely recommend.