Good, I like it when my players are disappointed!
Okay, seriously, the thing is, various characters are involved in the mod - and, more importantly, other mods can influence Assassinations, too. The Order of the Radiant Heart may not be available... the temple of Lathander... the prison in Government District... back rooms in the Copper Coronet... The list is long. And adding "but if you kill Lethinian right away, not only will you be unable to do the Copper Coronet quest, but you will be cut off from quest 6a from Assassinations and quest blah-blah-blah from mod ABCD and also..." - which makes little sense. (Besides, I've done Mae'var hundreds of times, and the temple of Lathander became hostile only once or twice).
So, I am sorry for your loss, and I think this topic forewarns the unwary players nicely.