One of the prophecies given to Londo by the "seer" (played by Majel Barrett) was not to kill the one who is already dead.

That would seem to be an obvious reference to Sheridan after his return from Z'ha'dum. But when would he have had that opportunity? I can't think of an occasion when Sheridan's life after returning from Z'ha'dum might have been in Londo's... control?... but Londo didn't kill him, either by chance or because of remembering the prophecy.

The closest I can come is when during "War Without End," Sheridan "time-jumps" into the future and arrives at the palace on Centauri Prime. Londo claimed he would kill Sheridan then, for revenge, although that turned out to be just a threat to satisfy Londo's "keeper." But time-jumping Sheridan hadn't been to Z'ha'dum yet, so he wasn't "already dead."

Assuming Londo would not have known that, he would have assumed he was dealing with the "already dead" Sheridan, does that satisfy the prophecy?

Maybe it does.