The problem with the quest is that the Devs have removed most ways of killing the mobs under the grating. Even before they made these changes, the quest was extremely hard for melees. Additionally, the quest gets really frustrating if there is no trapper.
With that said, the quest being required to flag isn't the problem. The problem is the flagging itself because you must run every quest to run the flagging quest. Yes, you can window farm the final quest, but most people/groups won't stick around for multiple runs of Cursed Crypt. Yes you can get/make an opener also, but again it can be a pain.
If the flagging for Necro 1-3 was fixed so it's similar to other quest chains like Red Fens, I'm sure most complaints about this quest and those packs would disappear. The annoying quests would be an once and done for those who don't like them.
Aside: I'll throw Threnal's flagging in the Necro pack pile of flagging mechanics that need to be fixed so people can enjoy the packs a bit more. Of course, Threnal probably needs a bit more tinkering to make the pack more enjoyable, such as a real wilderness area and revamping the side quests into probably challenges, but that's a different discussion for a different thread.