After CIA Deputy Director Pamela Landy gets access to Treadstone files in The Bourne Supremacy, how does she conclude that Ward Abbott had Conklin killed? I think that if Abbott wanted to clean it up, he should have killed Nicky and Jarda as well. When she confronts Abbott he doesn't even deny it. Is it permissible for a CIA senior officer to take out one of their own?
She suspected that he did because Conklin was making a mess as he attempted to capture Bourne.
When first questioned, he denies it, but because Landy read the files, she knew Abbott was in charge and that Conklin reported to him. He decides to tell her what happened, about Bourne failing a mission, and how Conklin couldn't bring him in.
Is it permissible for a CIA senior officer to take out one of their own?
Remember that Treadstone is a highly top secret black ops team. With Conklin failing, Bourne on the run and the dictator talking about an assassination attempt, it was becoming too public, too fast. Obviously the CIA didn't want any links back to them, and if it became public, then the CIA would come under review. This happened at the end of The Bourne Ultimatum. To keep everything secret, Abbott killed Conklin and lied to congress about what Treadstone really was. While not allowed, Landy understood why.