I had this problem earlier tonight myself. What I did on the next run-through after deleting the bugged character, was to wait until red alert went off, and to make sure the text blurb showed up between finishing the ground and beaming back up. I got the text blurb, and the mission completed fine.
I'm starting to think the bug might be similar to one I've had in Night of the Comet, where a text box not seen and acknowledged can cause the whole mission to foul in the bar brawl. Basically, same deal to fix, just take your time between the first group and the bar, and it'll pop up when you aren't on red alert for the ground map.