You cant say they just like animal, reducing budget will kill them, even more it allow them more time to escape the inevitable. Unfortunately for the welfare agency this is an opportunity which the government are hoping for, capturing Giacomo and at the same time destroy the agency by accusing them as a anti-government force.
You say why not just abolish the agency. But just like any government in every nation do you expect them to obey and not hoping for backlash especially when it came from assassin cyborg.
A simple fundamental is, government who reducing it military size, will create unemployment for them and this in some will seek personal vendetta, sell classified intel and worst use their military training to help other army and anti-government force.
So yeah, a quick way to eliminate threat is like always silencing anyone who could post a threat forever.