First, women used to take self-defense, while the men took boxing freshman year. Everyone has two gos of unarmed combat in their upperclass years. And to be clear, while probably safer than boxing, self-defense racked up plenty of injuries. I myself ended up with a nasty ankle sprain that sidelined me for a couple months (my significantly larger sparring partner incorrectly executed a move and ended up throwing me on my ankle) and nearly ended my tennis career before it even started. Unarmed combat is no walk in the park either - lots of injuries coming out of that class.
As for why it's still around, i'd say it's one of those entrenched rites of passage that is unlikely to go anywhere. That said, while I definitely see the valuable lessons learned in boxing (how to take a hit, refocus and push through it is a valuable skill set for sure), I'd argue with what we know about the risk of concussions and lasting damage, it's likely not worth it in the end. It is entrenched in tradition at West Point and Navy, and USAFA wasn't far behind though, so getting rid of such a long lasting tradition is just hard.
My guess is that if someone compiled the actual data on concussions and injuries from the class over several years, it would be pretty compelling. But I'm not optimistic - we have known for at least decade, probably two, that football is incredibly dangerous, but it is still a widespread sport that doesn't seem to be going anywhere.