It says they removed him after he finished praying-- it seems like removing him would have delayed the flight longer than just letting him take his seat at that point.
My guess would be that the FA thought that he was a threat to security. We weren't there perhaps theres something were missing. Lets consider this from a few sides.
1. FA: Passenger is not obeying the cabin crew which, under law, passengers must obey.
2. Passenger: "All I need is a few minutes to pray to God."
3. United: We need to get this plane off the ground so we can report an on-time departure.
I highly doubt the situation would've been any different had the passenger been the Pope himself praying in the corner or a buddhist meditating. The crew is the authority on board and it was their decision to remove the passenger. They could've asked the cops to arrest him. Instead, they put him on a later flight. I'm not condoning the FA's actions or UA's actions, but they could've been a lot harsher with this passenger.
Plain and simple, God is important to the religious. But when you're on board, weather its God or call of nature, you need to be in your seat when that door gets shut. Or else they will kick you off.