And if he'd pulled Allen after one quarter he would have been criticized for not giving him a whole half with the starters, as was the plan. Some people would have said he obviously thought Allen wasn't looking good and so pulled the plug on him, others would have accused him of being over-protective and instead throwing Peterman to the wolves.
Maybe he left Allen in for the second quarter because he wanted to see how he'd handle the adversity he saw in the first quarter. In fact I believe if he hadn't hit his head at the end of the half he might have even put him out there for one series after halftime, just to give him the experience of that.