I know this is "late to the party" so to speak but I'm going through and doing some mopping up. This is how I did it and it worked perfectly because I'm on 2nd play through and have a fully upgraded Contact Beam and the stasis was preventing them from being knocked back PLUS it was killing them instantly. So if this is you and you're having trouble, try this.
I played on casual until I got to wear Isaac sees the ships taking off through the huge windows (ch. 2) A few minutes later you'll come across you're 1st work bench, PASS IT UP. Go through the door, kill a few necros and there's a save station right there to the left. Save. Change difficulty to Zealot, go back to the bench and unload all the power nodes from Contact Beam. I reinserted for capacity and reload because I wasn't sure it would work but it did the 1st try so you don't even need to do this.
Go back and PASS by the save station and go through the door where you'll be in a hallway. To the right there's some necros terrorizing citizens through a busted wall, you'll see one morph and then walk off to the left of the screen. Turn back and face the hallway, about 15 seconds later that same necro comes for you. Use your Alt beam then charge and kill, you dont even need to stasis it 1st. Then if you're going for more mop ups like I was, just reload the check point and it'll take you back to where I 1st told you to save and your Contact will be back to full upgraded and back on whatever difficulty you were playing on. Good luck, hope this helps. It took less than 5 minutes when I got to the area.