That would certainly make sense. At the beginning of ToB, the elves in Suldanesselar began giving you sideways glances, no doubt thinking of the potential threat you were, if not directly from you, from the other Bhaalspawn who would inevitably come to hunt you down. Given the existence of the almighty grapevine, both Athkatla and Trademeet would no doubt know of you heritage by then. At least, a few of the smarter higher-ups would be able to put two and two together. You did take out Sarevok, and it's rather well known you had a somewhat personal stake in the matter.
Now, considering you'll probably have saved Trademeet, I could imagine that they would be a tad more understanding than Athkatla, in which your actions did not have a profound impact upon the decision-makers, aside from the rather drastic loss of the power the Roenalls would have suffered, which I doubt would put you in the good graces of the higher-ups. But even in Trademeet, the priority would be to protect the city, and hey, you already got paid. Lots.
As for the keep, it's entirely possible that you might have to go back and defend it, but on the other hand, the Five have already found you. Illasera takes you on in the forest, Yaga-Shura is already sieging Saradush, Abazigal and Sendai have other things that they're busy with, and Balthazar... is an LG monk (not entirely certain of the alignment, correct me if I'm wrong). Assaulting your keep just to get at you when you're right there in Amkethran doesn't quite fit his character. Therefore, it's entirely possible that to ensure the safety of your keep, you'd best stay the heck away from it. Nalia might even say as much. She's a bit naive but by no means stupid.
(plus, it would mean fewer headaches and a faster completion time)