I'm at part 3 where you have to disrupt the beams. I've beaten the room where you have to displace those boxes to fix the beam and I've done that and killed everybody. According to a walkthrough I saw the next open door should be to the left but there isn't one there or anywhere else in the room. I've gone back to the checkpoint a few times with the same result... have I hit a glitch or am I missing something? Should I restart the whole mission?

I'd say restart the whole mission. I had no problems at that point.