The Emperor not being malicious is debatable and probably depends on one's personal definition of malice. I'd say that it simply does not have the player group's best interest in mind. It knows from the start that we are looking for a cure and want to prevent ceremorphosis, still it encourages us to use and devour tadpoles, despite knowing this will later make it harder for us to resist the special Astral tadpole which it is preparing for us.
Of course this is related to its believe that we need to become more powerful in order to defeat the Absolute, but still this manipulation directly contradicts our most important goal - or at least one of our most important goals, depending on your character. So, it's very simple, I don't distrust the Emperor because it is a mind flayer but because it tries to sabotage one of our main objectives. By contrast, I have no problem trusting Omeluum.
