Well, the obvious question that you need to go back and answer before moving any further with this subject is whose viewpoint we're discussing. One imagines that the generation(s) of humans who survived the war will not easily forgive the Emperor... and that after they pass on historians will offer increasingly complex academic reads of his role in the war itself.
... but Kilrathi are a different story. The Emperor is based very much on the Japanese Emperor from World War 2, whose involvement in the war is historically amorphous and who was never (to this day) questioned by the Japanese people.
This is more than simply a question of 'what did he do', but rather is one which addresses the basic makeup of their system. If an Emperor is appointed by God (or Sivar or whichever part of the Kilrathi pantheon is responsible for such things) then how much can you criticize him? The fact that the Cult of Sivar is still active (and emblematic) in 2681 tells us that the Kilrathi religion *didn't* fall apart.
(But we also know it was strained - look at the Blair cult that Melek belonged to... that's definately an attempt to reason within their system how the Empire could have been so wrong.)
You mention the Kilrathi Civil War, but you fail to consider that the factions are fighting to prove themselves worth of taking the lost Emperor's place, not to reinvent Kilrathi society in some way. Kils are fighting to prove that they're worthy of the Kiranka lineage, not to distance themselves from it.
You also mention the rebellions... lets remember that we very, very rarely see how actual Kilrathi civilians feel about their Emperor. In so far as we can tell, they were loyal to the last (many suicided after the war for this reason.) (And of course it's hard to label an Emperor terrible simply because rebellion occured in his reign... else Lincoln fairs very poorly in our own history.)
We have a skewed viewpoint, getting 'inside the head' of social climbers and Kilrathi who are tainted by human culture rather than the everykil. Make no mistake - our favorite Baron was exactly as 'ruined' by human culture as he was accused of being in Fleet Action. We may be sympathetic to him, but we also must recognize that he was the way he was because of an exposure to human beliefs. Ghorah Khar's society finding fault with human slavery falls into the same category. These are forced breaks with the whole of Kilrathi society rather than some internalized conflict supported by the masses.
