I believe that taking a Marine who's not quite up to the job and shipping him of to some other assignment puts lives in danger.
Jessup is not a man who is in favor of keeping the weakest link as a part of the chain. Instead, he favors making sure that the entire chain is strong, so that there are no weak links for it to support. This in some way goes to explain why he was ready to give the Code Red order with regard to Santiago; having already requested a transfer and identified himself as a man who could not, and was not willing to, work with his unit, Santiago had also alerted Jessup to the fact that he definitely showed weak link potential.
Jessup felt Santiago was not up to the job on any assignment and ordered the Code Red to try to bring him in line and make him do better, and fit in more with the unit. He does not believe that he is in the wrong, because he believes that if hs is saving the lives of other Marines, he is doing the right thing, however he achieves that end.
Jessup : "I'll answer the question. You want answers?"
Kaffee : "I think I'm entitled to it."
Jessup : "You want answers?"
Kaffee : "I want the truth!"
Jessup : "You can't handle the truth!"
This is perhaps one of the most iconic lines in movie history, and it is the pivotal point of a heated exchange during Kaffee's cross examination of Colonel Jessup. Having managed to catch Jessup in an inconsistency about who gave the order for the Code Read, Kaffee wants to know who actually gave the order and where they were given the authority to do so.
Jessup genuinely believes that unless someone has served in the Marines they should not question his actions. He provides them with safety and security and does not feel that the manner in which this is done should be questioned by outsiders. He is a proud man. He feels that Santiago's death was a tragedy but that it was for the greater good because had he been put on an assignment, his lack of skill and inability to be part of the cohesive unit would have put more lives in danger. Jessup sees himself as a man who keeps the nation safe and therefore does not appreciate the nation questioning what actions he takes in order to do so.
