Disclaimer : I don't own stargate SG-1.
Five reason Sam still run and work out several time a week in Atlantis even through she's not on a field team any more.
1/ Because in the stragate business the battlefield has a nasty tendency to follow you everywhere and if the SGC and Atlantis have a motto its "Be prepared for anything, because anything and everything will happen.".
2/ Because she's not twenty anymore, her metabolism is starting to slow down and there is no way in hell she'll start a diet.
3/ Because she's not twenty anymore and for some reason her body is not as forgiving as it used to be about spending the night at a desk or under some piece of equipment. The exercise prevent her muscles from becoming too sore.
4/ Because it give her an occasion to interact with the people under her command in a informal setting, and she needs all the help she can get to integrate.
5/ Because she spent the ten years on a team that traveled to planets light years away from earth for a living.
Psychiatrist after psychiatrist marvelled at SG-1's ability to seemingly shrug of the stress and the trauma that came with it. Now that she's flying a desk Sam wonder I maybe they got too used to the stress.
The adrenaline fix, she get from being responsible for the live of some of the best scientist and soldier the Earth has to offer in a city where one crisis end when another come knocking.
The endorphin fix, she take wherever she can get.