Tosh.
I don't even know what you're talking about with 1 and 2, unless it's "the game lets you act like a murderous mercenary thug if you choose, instead of putting you on you're-the-hero rails like some much older CRPGs." For 3, the game does try to hard-sell you "the fact that you've killed all these people proves you're the inherently evil child of the God of Murder," but unless you've been choosing to act like a murderous mercenary thug (hmm...), you can look back at everyone you've killed and know that, just like in the significantly-higher-body-count Icewind Dale games, they all attacked you or someone else first, making the case better that they were all "children of the literal God of Murder" and thus driven to murder, than that you are. And then, for all Throne of Bhaal's failings, you can become a god of pure good based on your choices*, and you're not tilted toward becoming a god of evil if you choose to ascend.
*Again--unless you've been clicking the "I am a murderous mercenary thug" dialogue options. Hm, I might know why you described the game the way you did, after all...