Here's my take on the Irenicus/Tree of Life scene:
I don't find it surprising that Irenicus doesn't go hostile on you prior to destroying the last parasite as he is deeply involved in concentrating on draining the Tree. He is only disturbed when you slay the last parasite and even then seems groggy (reference the dialogue).
He is fairly weak in fighting you as well because of your disruption of the ritual. Now, with that said...
If you choose to use "cheese" tactics, then that is your prerogative, however, the battle is meant to be fought face-to-face. I agree that Irenicus should be inaccessible prior to him confronting you, but it didn't work like that so it is upon the players to avoid using too much cheese.
As for dragons:
The designers at Black Isle have stated that they are making some significant changes to dragon AI. I don't expect that there will be much opportunity for cheese after they make their modifications. Seeing as they had around 50"ish" responses on the Black Isle board as to, "What do we need to change relating to making dragons more challenging?". I think that all cheese was covered there...
So...don't try that trap crap (hey...I'm a poet and didn't know it) in ToB or your thief will be a dragon toothpick.
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Now where did I leave that doughnut?!