Insurgency
Tarrlok was a long-time opponent of the Equalist Movement. Removing his bending was advantageous for Amon and his insurgency group. It would prevent Tarrlok from effectively leading the – or any – counter-Equalist force in the future.
Secrecy
As soon as Amon resisted Tarrlok's bloodbending, it would be apparent that Amon was in fact Noatak. Tarrlok would at least have suspicions. Keeping Tarrlok as prisoner was, at this point, essential, in order to keep his identity secret from the People, most imperatively Equalists who followed him.
Practicality
As a waterbender, Tarrlok was too dangerous to keep, even in a metal or wooden prison. As a bloodbender, it was completely unthinkable. In keeping with Amon's cautious and pragmatic personality, taking away Tarrlok's waterbending away altogether was the only way to ensure that Tarrlok was ultimately zero threat to Amon's followers or to the privacy of his identity.