Why do you hold the CIA in partcular fault for the Iraq War - it was the Presidential administration that drove us there and it was White House "leadership" driving the aspects of CIA bad behavior.
I don't claim to have a clue about Slotkin's CIA work, but in as general proposition, large institutions are generally bigger and greyer than their individual actions. The CIA was an arm of a basically outlaw administration, but as we saw with the Trump admin - it's sometimes a lot better in the long run if some good people stay and throw what sand they can in the gears of the bad actors than to just all flee and leave the field to the baddies. Like a lot of things - it's situational. A high profile resignation can be politically signficant. At the analyst level maybe all that happens is the replacement is a more ideologically driven flack less likely to generate reliable intelligence.
Unless you are self employed you aren't likely to ever go very long in a career before you disagree with the ethics of your employer. What you do about it will often depend on how much freedom you happen to have to not participate in what you don't like and how much positive value you think you bring in spite of the company.