Thomson was originally relegated to the pen this year but with Ramirez going down and the rest of the starters in shambles through their first 1 or 2 starts they were forced to put him in the rotation, so for his first start I'm not surprised to see him pitch 5 and leave.
Not to mention he smacked a double and was running the bases for awhile, after spending the offseason and spring training preparing to work in the bullpen and not practicing hitting or conditioning as if he were pitching/hitting/running for 5-7 innings I think it's the best decision.
Now they just have to hope someone in their bullpen will step up for a couple of innings...