The whole thing seemed odd to me. Imprisoning them and refreezing seemed like the obvious choice. Why take the chance that a random ship stops by, detects life, and goes down for a visit only for Khan and company to commandeer it for their own purposes.
I mean that must have been a viable option. If it wasn't because Khan and his crew so much stronger and more intelligent then they would have simply just taken the ship, why agree to be stranded?