The best way to discard Jimmy is to let him leave the CIA directly. Using Caitlin's network, retiring an agent is still achievable, though it might come at some cost, owing some favors. As a senior executive, Caitlin naturally has people above to take care of her. Owing some favors is not a big deal; the key is whether it's worth it.
The second option is to put it aside and not use Jimmy anymore. This time should be his last mission, but whether Jimmy can accept it is something she needs to consider. This mission still needs to be archived, making it even harder to bridge the gap between both sides.
Finally, there's the option of elimination, but this idea never took root in Caitlin's mind and vanished as quickly as it came. She is well aware of the things Jimmy has done before. Whether it was the attack in New York or activities elsewhere, they all indicated that elimination was an absolutely unacceptable option, and she currently didn't have suitable personnel to handle it.
