Brown Rice vs White Rice in Stuffed Pepper
Brown rice takes considerably longer to cook than white rice, and requires a higher ratio of liquid to rice. 

It may be somewhat helpful to pre-soak the brown rice, but that may not completely compensate for the longer cooking time. 

The main issue is going to be getting the rice fully hydrated and cooked through without badly overcooking the peppers.  

Your best bet is probably to start with cooked brown rice, which my survey having googled "brown rice stuffed pepper recipe" indicates is the most common method, although they don't generally employ a crock pot.

For a one-step fully crock-pot based recipe, white rice may be indicated.