Hayate's PoV is that:Even after Hayate was told about what that fucker did she has his photo in her family photo album.
-Without him she'd still be the Book of Darkness's master. He identified her, but the book's master assignment is not under his control.
-Which meant she'd be a terminally ill, crippled orphan until the Book activates.
Instead she has a good standard of living, the ability to attend school and the ability to pay for all the special needs she has.
Maybe it'd be better if he had been open about it, but she does owe him pretty badly from her PoV.
Keep in mind, even their "investigation mission" ships carry an Arc-en-Ciel, which is a Superweapon in its own right. Specifically for "the only way to be sure" scenarios.
Spatial Distortion cannon is apocalyptic when fired in atmosphere yeah...