I would NOT prune.
I NEVER prune my hot peppers!
Once, I over-wintered a hot pepper, and a lot of the top died back... it was coming on gang-busters from below, so... I pruned back the old growth...
killed it.
If you have new growth... enjoy it. when you set the plant(s) out in the garden, the new growth should start producing peppers for you waaaay faster than new plants.