CHARNAME's opportunities to kill Tamoko are outside the Flaming Fist headquarters and in the Undercity, neither of which are anywhere near the Black Dragon Gate, and it's hardly likely that the party would kill her in a way that would leave "NO OVERT SIGNS OF VIOLENCE, DISEASE, OR DECAY."
We had to juggle the jigsaw somehow to match the ToB (epilogue) assumption: one way or another, Tamoko is dead. The tricky part is, of course, that we don't know when, where, or how she died, or if it was the PC who killed her.
I'm not sure that this is the optimal juggle, but it seemed functional enough. If you have suggestions on how to improve it, though, please don't be coy.
I think a better place for her body to be found would be the Undercity. Assuming that the party didn't kill her in the encounter outside the Flaming Fist, she heads down there and could quite logically be killed by either
a) The party, for trying to stop their quest to kill Sarevok,
b) The group sent by the Iron Throne, because she's one of Sarevok's followers,
c) Some contingent from Baldur's Gate, sent to scour the place for any of Sarevok's minions,
d) Sarevok himself, in his mad rage, or even
e) Irenicus, Bodhi, or any assorted minions, who may have been watching from the sidelines: An opportunity to capture 2 Bhaalspawn (or even 3, given the presence of Imoen) for the price of 1? Count me in.
Of course, of these people, only Irenicus or Bodhi could have killed her without apparently doing her any physical harm (Finger of Death / Rapture of the Father and Level Drain, respectively), and they're the ones with the lowest odds of being present. So perhaps the 'death by unknown magical means' should be dropped. The incorruptibility of her corpse also tends to cause misleading ideas of resurrecting her, and is, in my opinion, unnecessary, so I think that should be dropped too. A man's quest to avenge his murdered sister is dramatic enough without additional mysterious and unexplained circumstances.
Your idea to have Yoshimo obliquely probe CHARNAME on the issues of mercy and forgiveness is a good one.