I watched the sneak peek and at first it got me thinking that Regina would never let Henry go like that. She even expresses her disbelief that Emma agreed to this, but then I remembered how Regina was treated by Cora when she was the same age. Forced into a marriage she didn’t want. Forced to take on a role she never asked for. Forced to be someone who she never wanted to be.
That reminds me that Regina broke the cycle of bad choices that started (as far as I remember) with Cora and it was almost perpetuated when she became reactive when Emma appeared in their lives.
However, that staircase scene in 2.02 is proof enough to me that Regina would never cling too hard again because she knows more than anyone how this ends up pushing people away. Of course the mother does not want to let her little prince leave, but she remembers what imposing her wishes upon him did to both of them (and to her when she was young) and how long it took for Henry to come back home on his own.
So it doesn’t sound strange to me that she lets him go find his own story. Her heart is probably small and it will be for as long as he’s gone, but she knows you can’t keep your babies forever under your wings.