As Daphne let loose the arrow and took off running two things occurred to Apollo. First, if Daphne got away she'd alert Artemis as to what Apollo had done, and two, the little nymph was still a ridiculously fast runner. However, this time all the praying in the world wouldn't save her as he spared a glance at Ate to make sure she was alright before setting off after the nymph.
He knew that if Ate caught her first the struggle to keep her from ripping the nymph to shreds would be epic, and while he had promised Ate a little enjoyment he didn't want Daphne to be too hurt when he finally subdued her. Still, Ate deserved a little revenge after what had happened.