In final scenes of Alien: Covenant, the alien enters the ship and kills Upworth and Ricks. Mother alarms all the crewmembers about it. So Daniels and Tennessee kill the alien with David's help. Why would David help kill the alien when he greatly dislikes the human race?
I believe that David, in this case, is making a sacrifice of a single Xenomorph in order to better spread the Xenomorph race to the new colony world. As he states to Daniels (albeit in a context where she doesn't understand his meaning):
"But that’s what we’re doing too, isn’t it? Creating a new world on Origae-6 ... Honestly, I could use a new world."
And further direction from the script:
David strides in. The Colonists. Tier after tier after tier of them in hypersleep.
Also the rows of embryos.
He walks forward.
Gazing up at the sleeping Colonists.
His children. His slaves. His subjects. His.
The Wagner swells. Grand and triumphant.
And David smiles.
Dreaming of the future.
I ran into a second good theory here. David has been doing his experiments to create the ultimate predator species and the deleted prequel scenes show that he's gone through several generations that were not sufficiently advanced for his purposes. He may have aided Daniels and Tennessee in defeating the creature because he wanted a more challenging test, one which it didn't quite overcome, although now he has more subjects to work with, including Daniels, who he may be targeting to create the first Queen.