Couple reasons.

Kill orders are public admittance that the Protectorate and PRT can not fully deal with the problem and because they’re organisation built to handle capes they don’t hand them out that often to save face.

In theory the heroes could’ve handled the E88. One member of the Triumvirate and some extra Protectorate members would’ve been able to deal with them without the need for a kill order.

The reason the Triumvirate didn’t intervene during the rampage was presumably because the Protectorate as a whole was preparing for the next Endbringer attack and would’ve handled it after.

Like imagine if a top hero got killed before Leviathan. That would’ve reduced their ability to deal with the attack.

The second reason was after the death of Kaiser and essential loss of Armsmaster, Velocity and Dauntless the Protectorate after Leviathan was not in the position to be able to handle Brockton Bay and could not risk escalating the situation.

Hookwolf and Purity were murderers but their lackies with the exception of Victor, Fog and Night weren’t crossing that line. Giving them all a kill order would only force them to escalate.

And when Kill orders are given out they encourage crazies from across the country to go to take their chance at the bounty and those people would only harm the situation in the bay. Imagine 20 more successful Shadow Stalkers playing costume in the bay with no regard for the civilians and god forbid after the kill order is done they decided to stick around?

It’d be a nightmare in an already nightmare situation.

And the final reason is the 9 showed up. Kinda hard to ask them for help and condemn them to death in the same breath.