The Doctor's comment to the alien Tim Shaw that it should return home (after having set off the bombs inside itself) would strongly suggest that with the appropriate medical treatment, that the DNA bombs shouldn't be fatal. Since it had no choice but to comply and had stopped actively trying to kill them, that was tantamount to admitting defeat.
Doctor: You got everything transferred to you including five tiny bombs. You had a choice. You did this to yourself.
[ALIEN SCREAMS]
Go home.
In essence, he was killing an enemy that had already surrendered.
