Second-half strikes from Jermaine Easter and Aaron Wilbraham fired the in-form Dons to their fourth straight win and sent Gills down the League One table to 16th.
But Stimson said: "It was a decent performance from us and I thought Matt Fry was outstanding on his league debut.
"Their second goal was one hell of a strike, we had a couple of chances like that which went straight at the keeper.
"We did our job in the first half to keep it 0-0, but if we keep performing like that away from home we will start winning games."
He added: "Scott Vernon is leaving the ground on crutches so lady luck has not smiled on us, his ankle is swollen."