Those are really good points. I've never seen anyone presenting those before, in all the time I've followed the game's history. And they are correct (except about Irenicus, isn't it in Spellhold Maze Bodhi says she's not afraid of him.)
A short-term fix would be to comment out the encounter.
In the long run, someone can script it differently: maybe a dialogue, no-fight; maybe a separate component.
For the third I would beg to differ (at least in my mind) because Irenicus:
1) Carefully chose you amongst all the Bhaalspawns
2) Had you imprisoned for a long time and experimented on you
3) Actually hired the thieves guild to get you (and he usually acts methodically and efficiently: this means he actually exposed himself and he would never do that if he is not sure that his plans would come to fruition)
4) Had a base he set up to do all these things
5) Was able to actually hide for all these years
6) Got discovered because of the mess that happened over the promenade (and I'm not totally sure, but I seem to remember that it was implied he did that on purpose)
Imagine if Bodhi killed charname after all the time Irenicus spent on you. I don't think him to be so lenient when there are errors involved and he actually is all but forgiving (especially in the matter that he is trying to fix: just see what he did to the two elves when he met them in person in front of the drow matriarch).
Beside, in my opinion, Bodhi does the big talking, but she is not as strong as the brother.