This was one of the things that baffled me in book 1. When Amon releases Tarrlok from prison, he shows regret and apologises for taking Tarrlok's bending. He clearly still cares for his brother at this point. Why did he take his bending, Considering how powerful he was, he could have just knocked him out. I don't get it.
Tarlok was Amon's brother, so he didn't want to kill him; he couldn't release him, because then Tarlok could reveal that he was a bloodbender; since Tarlok was a bloodbender, the only one who could prevent him from escaping would be Amon himself, and that would run the risk of revealing himself as a bloodbender. Since he was the head of an anti-bender movement, being outed as a bloodbender would be rather bad (indeed, the revelation that he was a waterbender seemed to kill the Equalist movement pretty quickly).
So it seems that his only choice was to remove Tarlok's bending.