IDidn't Sif say her voice casts a spells? Maybe he was under a spell the second she spoke. Plus, if Ward took Lorelei as being similar to Loki, shooting her and failing may have resulted in him getting stabbed like Coulson. I think he was using himself as bait, non-threatening, for Sif to finish her off. .
Lorelei very clearly didn't speak at first, the director was obviously building tension there. Ward actually had plenty of time to turn around and run, and I seriously wondered if he wasn't staying on purpose, thinking he would be able to resist.
Meanwhile, exactly why not shoot? Why not shoot 8 or 10 times if she is a tough Asgardian? He has nothing to gain by not shooting, and nothing to gain by not calling out for Sif.
I would have found it more believable if he'd shot and the gun did nothing. Fine. I would have found it more believable if he'd dropped the gun and put his hands up. Just pointing and saying "OK, turn around and get on your knees" (which is what actually happened) was ridiculous, because it indicates that Ward actually believed his gun was a threat to her, but he didn't use it.
Again, I felt during that scene that Ward wanted her to use her powers on him, (Asgardian berserker feelings maybe?)
If the Bus could get there in x amount of time, then at least a couple of female SHIELD agents could have gotten their. They are masters of logistics, after all. Form a double ring with female agents in the centre and males with rifles on the outside, wearing head phones.
But of course there needed to be a plot.