Hook is not exactly a child friendly guy. He is too focussed on his revenge against Rumple to care about who gets hurt in the crossfire. Henry would just be collateral damage.
All of the characters of Once have something in common with their literary counterparts and you can see how the tales we know could’ve come about even though they are not entirely correct according to the show. For example, Rumple still spins straw into gold and makes deals like he did in the original tale of Rumplestiltskin. The two big things about Hook are that his hand was taken by a crocodile and he is mortal enemies with Peter Pan. Once has already done its twist on Hook losing his hand to a “crocodile” but has not yet covered the Hook/Peter rivalry.
Why would our version of Peter Pan have Hook trying to kill Peter Pan when in “reality” Hook wouldn’t hurt a child?
All magic comes with a price!
Keeper of Felix