con-: together, with
sist: derived from Latin "sistere", meaning "stand"
-ory: the place of doing something
So consistory means:
The place of standing together.
It means "the place (church) where priests stand together to judge whether one person is guilty".
Evolution of usage
The place of (priests) standing together had a lot of power in ancient time.
The consistory had a lot of power in ancient time.