I'm sure you'd be able to customize the order to have less calories.
I've never been to Chipotle, but here are a couple items I customized on their website the way I would eat them:
Burrito: Sofritas, brown rice, black beans, and fajita vegetables - 785 calories
Burrito Bowl: Sofritas, brown rice, pinto beans, fajita vegetables, fresh tomato salsa - 500 calories
From what I've heard, the meal sizes at Chipotle are quite big, so no need to add any sides.
"We have enslaved the rest of the animal creation, and have treated our distant cousins in fur and feathers so badly that beyond doubt, if they were able to formulate a religion, they would depict the Devil in human form." - William Ralphe Inge