Off-Topic: A question about A Few Good Men for military folks

Don't ask me why, but I was thinking about the movie "A Few Good Men" this morning, and something has always bothered me about it.

As you'll recall, the reason Private First Class William Santiago was given the Code Red in the first place is because a) he broke the chain of command by begging everyone in the world to transfer him out of Guantanamo Bay, and b) he offered to squeal about the "fenceline incident" in return for the transfer.

OK, fair enough. But the scene which bothers me is this one, which is also the introduction to Col. Jessup:

Here's my problem: As Jessup clearly states, PFC Santiago was, by all accounts, just a shitty Marine. He simply couldn't keep up with the training. Regardless of whether it was because of a legitimate medical condition or due to him "not being properly motivated", he couldn't hack it, end of story. Furthermore, no one liked him anyway.

Jessup doesn't want to transfer him because then he'd just be some other Colonel's problem, and he doesn't want to weaken the Marines by letting quality control slip. OK, I can accept that.

However, my question is...why was he kept in the Marines at all? Couldn't he have simply been discharged for not being up to the standards of the U.S. Marines? That would have solved Santiago's problem and the base's problem without "jeopardizing" the rest of the Marine Corps.

I'm not being snarky here...I know nothing about how military procedure or protocol works, but I presume that if someone is incapable of meeting the physical requirements beyond a certain time period that they're simply kicked out.

Or am I missing something obvious here?