[@BlackSam3091] His Cerberus Evals have been under wraps for quite a time. i doubt the Council has someone with access to them. His xenophobia is damaged by his newfound desire to be good. He understands that xenophobia is irrational, but finds it difficult to fight it. That having been said, he filters himself quite well, as he had to learn to do, in order to achieve a number of desired ends. Without his watching his words and tone, he would be much less of a viable candidate. As is, and so far as the Council has information, they believe him to be dangerous, but nearly as unstable as he is. That having been said, his new epiphany, and this new infatuation, no doubt catalyzed by said epiphany, will likely solidify his loyalty. 
Despite how many problems he may have, he never once disobeyed the Illusive Man, and his psychotic loyalty is a big asset to the Spectres. His true value comes not from his strength, combat prowess, or resilience, it stems from his inability to disobey those in authority above him, no doubt sourcing itself in his childhood, wherein first, there was his father, who was certain to impose strict rules to maintain his career. Second was his brother, who watched over him and looked after him while he was helpless. Then, the Illusive Man, a man with power so great, it was nearly impossible for anyone to refuse his demands.
On top of that, Ellis has detailed knowledge of Cerberus technology and tactics, and will be a big advantage against Cerberus forces for that reason, as well as the fact that they may recognize him, and put two and two together. More than anyone, Cerberus ground troops know the capabilities of Ellis the Undying. They once rallied behind him in battle, but when he is on the opposite side, they will gaze upon him in awe and horror, remembering the atrocities he once committed under their flag.

Oh, and it was all teased in the CS. It was in the backstory. I may have hidden these things in too subtle a manner, for example, I used the concept of him being bedridden and utilizing his biotic abilities in a way that felt aas though it manifested outside himself to represent disassociative disorder, indicating that he felt, though in control of his actions in reality, as though he were not committing them. His love for psychological warfare comes from the fear he felt as a child, no father, crippled, ruined, disfigured. He desires to inflict the same terror on others, a form of displaced Psychosis. His paranoia stems from all the information he sold, making enemy after enemy after enemy. His sociopathic tendencies come from his isolation during his developmental years. The bipolar disorder from a skewed reward-system in his brain that associates a satisfying kill with lots of dopamine, conflicting with his true moral beliefs, wherein deep down he knows that slaughter should not make him feel good, that war is inherently a bad thing, yet he loves it because it allows him to expend a lot of psychological stress.

In short, if you give the guy things to shoot and stab and strangle every now and again, he'll be alright. 

EDIT: Oh, and I'm trying to keep Ellis' turmoil from interfering with the others, which is why its all happening in his head. I hope that's fine. I'm having fun writing someone so self-deprecating.