Contact - TUBE FLARING TUBE FLARE ORFS FLARE 37 FLARE 45 FLARE

Before dying, John tells Dean, if he can't save Sam, he'll have to kill him, should he become evil. The fourth season episode "On the Head of a Pin" reveals that the demon Alastair tortured John in Hell for over a century, with John refusing the demon's offer to stop if he himself would torture someone else.

So, there are basically two reasons, both closely related to his sons: His own efficiency, as they get him distracted, for he goes after a dangerous daemon (the yellow-eyed one), and thus worries about them getting killed. He is afraid to actually see them die, like he saw their mother die.