The relationship between Rumple and his father is so deep and complex, it’s confusing. If he dies, I die. Very complex, and very confusing.
We know that Malcolm created Neverland through his lovely thoughts, dreams, and belief. It was meant to be a magical place. Malcolm was portrayed as selfish, juvenile, a dreamer and a scoundrel. He was a poor father, but in my opinion, he was not portrayed as evil. Bad guy yes, but he was weak, not evil.
However, just as Malcolm created Neverland in his boyhood imagination and belief, I think that Rumplestiltzkin actually helped create the evilness in Peter Pan. I think as a boy, in his not so lovely thoughts,dreams and belief, he came to know, and helped create, all the evilness we saw in Peter. Rumple believed it so strongly it became fact. His father was evil. An evil masterpiece created by Rumple.
He didn’t kill his father as he slept because Rumple himself was still posing. Still pretending he was stronger than his father. Still wanting to gloat, by trapping him in a box, by taking his magic. Still not wanting to acknowledge that it was time to kill, and let go of the evil he had helped create. He couldn’t kill his father until he truly believed he could.