You could also cheat your way in by teleporting to the area in question. Every area has a code, so it's fairly straight forward. Or you could just spawn the item in your inventory with the save game editor.
Maylander: Do you mean that you can access the keep as a non fighter before leaving the area after you are done with the quest? I don't usually take Nalia around myself so I can't remember clearly, but I think I couldn't get into the keep either straight after I've handed in the quest to captain outside or after I left the area.
I'm a very fast, sloppy gamer, so I often forget stuff. I've re-entered after completing the quest quite a few times, and I've been frustrated by the changing of the area almost as many times due to being a Fighter (or similar, like Monk). The keep remains a ruin with any loot or corpses or trolls/yuan-ti remaining if you're not a Fighter, but turns into this clean, nice place with empty containers and no corpses if it's the class stronghold.
UPDATE
I happen to have a ton of different save games on various computers available, so I just fired up several of them.
Using
BG2: EE I found the following:
Paladin with Nalia in the party, final chapter of the game, Nalia's quest completed:
Bumped into a guy called Quint Roenall at the gates of the castle, claiming I did not belong there. The side entrance was still open, but could not be entered.
Sorcerer without Nalia in the party, final chapter, Nalia's quest untouched:
Entered the castle without problems. Loot still present in the containers.
So it seems it's related to Nalia's quest. It has nothing to do with the EE. Also, this means that even completed Nalia's quest won't change anything - you'll still be locked out.
Basically, you now only have two options if you want the flail as far as I can tell: Spawn the item, or cheat travel to the original Keep zone.