Which quest is that? I assume you're not talking about the Gree event PvP quests, because those are clearly labeled as such. The only quest that really forces you to go into a PvP area is the HK-51 quest, where one of the parts is available only in Smuggler's Den on Tatooine. Further two quests require scanning a target within the area, but those can be seen from outside. Some Republic quests have targets south of Smuggler's Den, but you can access those through an unmarket tunnel from the Dune Sea.
I can agree that the tunnel could be marked. It took me a while to learn of its existence, and a good amount of exploring to find the entrance on the Dune Sea side. I don't see any reason why it should be unmarked.
It is the HK-51 quest and I think they should move that one part out of PVP area. The other quests is with macrobinoculars and Seeker Droid. I don't think any of them has to be in a PVP area.
Or perhaps I should just plan a coffee-break when I have to wait the 5 mins to be unflagged