Yes both Regina and Rumple have done horrible things in their past but Regina has also lied and manipulated Henry and made him feel crazy when he knew he wasn’t. Rumple hasn’t done that to Henry so Rumple is already at an advantage compared to Regina.
Also, Henry probably read about Rumple’s misdeeds before he actually spent time with Rumple. Now that he has spent some time with his newly discovered grandfather, Henry probably thinks Rumple isn’t that bad.
Henry knew Regina as his mother before he read the book. Discovering that the women who raised him had done all these evil things was probably a shock to the system for him. Not to mention all the lying, manipulating and deceiving she did.
All magic comes with a price!
Keeper of Felix