He did warned him against going outside, if you remember. Doctor knows he can't keep him detained forever because it's in our nature to want freedom and imprisonment means slowly killing the spirit. Imagine if you're in his position, would you let your selfishness take hold of you and detain someone (against their will) even if they're clearly unhappy about it, just to 'protect' them, or let them be free and happy even at the expense of their life? At least it's a short-lived happy life than long, unhappy life.
Also, leader did not 'own' the clinic, just like a president doesn't own the country they rule.
The leader is an 'immigrant' after killing the previous scientist who discovered the vaccines. He is a psychopath.
If you really wanna protect him,don't let him go outside in the first place!!
Not to mention this clinic is owned by someone know him as a zombie.
stupid doctor.