[quote=@Pathfinder]
[@Ruby]
Daniel is pretty easy to manipulate, but I don't see him being useful to her besides being a fleshy battering ram.
[/quote]

Daniel is a bridge between Children and Hydra.

That makes him fascinating to Alpha. 

If nothing else, I can see her inserting herself to calm him if he was going to kill someone besides Hydra, if none of the other Children stepped in. Likewise, it's possible he's one of the Children that the Institute believes communicates with Alpha on a level far beyond their reach, even if that communication is mostly along a primal level.

Lots of possibilities there.