I think, after WC1, her death was a lot less predictable than it seems in retrospect. Anyone who'd played WC1 beforehand would be used to characters getting killed only when he let them die - plus, he'd remember Paladin spending half the game talking about his upcoming retirement, and ultimately not getting killed.
Then there's the fact that this was the very first time ever that we actually saw a mid-flight cutscene in one of these games. Takeoffs and landings, briefings and debriefings, we'd seen that before - but the game wrenching control away in the middle of the mission? That was pretty shocking, and somehow, instead of taking away from the scene, it made it stronger. Had the game just tried to make you feel sad, it would fail - but seeing your character get mad about it worked perfectly. There you were, upset that the game designers killed a character and didn't let you do anything about it - and there was Blair, upset that Tolwyn let Shadow get killed. Those emotions worked together to boost the scene's impact.
...And finally, we were all much younger back then, and it was a different time

. We were much more willing to be impressed, especially since at this point, new games really blew us away, not with three more polys per character, but with completely new methods of storytelling.