Big Daddy wrote:
You don't protect a virus, you seek ways to neutralize and then annihilate it.
Not necessarily. Viruses can be reworked to create vaccines. Allowing Khan and his people to live keeps open the possibility- however remote- that they could be rehabilitated.
A sweet thought, but if after two hundred years in stasis, their first reaction is, "Hey, let's take over the universe" rehabilitation seems quite unlikely. Khan said it best himself in the episode:
KHAN: Captain, although your abilities intrigue me, you are quite honestly inferior. Mentally, physically. In fact, I am surprised how little improvement there has been in human evolution. Oh, there has been technical advancement, but, how little man himself has changed.
[my emphases] Yes, it appears we will do well in your century, Captain. Do you have any other questions?
Not exactly the kind of guy who sounds open to rehabilitation.
I do appreciate your position that all life should be protected, but I just don't think it is realistic when applied to people (whether real or fictional) like Khan. Thankfully, psychos of this caliber are in the very very tiny minority.