It's an MMO that is seeking to appeal to a broad range of players, who have varying tastes. For many, it is the antagonists who are more appealing than the protagonists in a story because they actually have genuine stakes, stand to lose much more upon defeat and generally have more compelling and complex motives. Final Fantasy VII - both the original and the remake - really appealed to me because it had such a strong range of interesting and memorable antagonists who weren't just unceremoniously killed off as the game progressed.

If the likes of Y'shtola can come back from the dead repeatedly, I don't see how it's unfair or unacceptable for the occasional antagonist to do the same thing. Provided it's handled reasonably well, of course and they're brought back to remain relevant to the ongoing story.