This is what I could immediately think of:
1) Depending on the location and what is created around the portal, a faction could easily go and block off everyone else from using the portal.
2) Possible spawn camping on the other side of the portal, if the Nether part of it remains a warzone.
1) Factions wouldn't be able to claim around the portal so that's not a problem, if people are standing and blocking it off by camping around it it's a good thing and the warzone portal is doing it's job.
2) This is a valid problem, I have no problem with people camping somewhere but the problem is the lag when you first get into the nether. It'd be better to have it like this than safezone though, there shouldn't be anywhere you can run to for instant safety. Any suggestions on how we can balance this?