I used my gene-modded colonel sniper for the covert operative, with a plasma pistol, the treats-half-cover-as-full-cover skill, double-tap, etc, and that is just terrifyingly effective. 'Course, it was still normal difficulty, so exalt wasn't very threatening unless they decided to use their rockets.
Edit: Oh, IIRC that bug can only happen on one of the two mission types (the extraction one, not the defend one), and you can save before launching the mission and reload if you get the extraction one, and it'll reroll it and potentially give you the other mission type. So you can avoid it entirely that way.
...Okay, the skill of the covert operative had nothing to do with anything. The operative I lost was a skilled assault who didn't take a single hit during the course of the mission, and indeed killed a few EXALT soldiers. We cleared the map of enemies, and I moved the operative into the evac zone. The mission ended immediately. Then when we got back to base, he randomly died. The result would have been the same whether the operative were a rookie or a gene-modded colonel.
THAT'S why I dislike fighting EXALT. Because their missions are buggy and soldiers can die completely at random. And I play Ironman, so no reloading to get a favorable mission type.