Yes, of course they're dead. Did someone question that?All I ask is that you recognize that no matter the difference in intentions and methods, the people you kill are just as dead.
As soon as you arrive in ToB, Ilasera attacks you. You can try to reason with her, and she tells you she and her allies will kill you. Then as soon as you land in Saradush, the very first thing you see is some of Gromnir's guards starting to cut down helpless peasants in the street. You can confirm it with practically anyone in town--"Gromnir killed my parents." "Gromnir lets his soldiers terrorize us." "Gromnir is even more of a tyrant than Count Santele." The only thing more obvious than Gromnir's need to be stopped is that Yaga-Shura is bombarding the town with fireballs. Even so, perhaps the PC thinks Yaga-Shura's been framed...that the army outside the walls answers to Melissan, perhaps. So the PC goes to his fortress--not breaks in, just walks in through the front door, and looks for someone to make an appointment with--and everyone attacks on sight. Similarly, Draconis and the disguised drow woodcutter don't wait for you to say "I'm here to kill my sibling"--they both spell out for you that their father or employer is wholly evil, and then they attack you.As the player, I am fully aware of the fact that the Five are 4/5 evil and 1/5 misguided. However, I don't know where the character gets this certainty from. You have the word of one woman, rumor and hearsay and some incidental writings (Yaga-Shura's journal). This is a rather thin pretext for breaking into people's fortresses.
Yes, it would be nice if the game gave the PC many more chances to try to settle things with words. Yes, the fate of Sendai's duergar slaves is tragic. Yes, the game presumes you have more faith in Melissan than any player likely would. But the game's demand that you feel guilty, that you accept you've been wrong to kill those people, is horribly contrived. Less violent means of conflict resolution aren't missing because you're the child of Bhaal, they're missing because the developers didn't want you to take them. You kill just as many people, for reasons no better, in games where you're defined as a pure-hearted hero descended from a long line of pure-hearted heroes.