Maybe it was all just pragmatic?
Let's say the decision is made to make sure Fisk goes to trial...how long does it take to even just select a jury?? With all the shenanigans his lawyers would throw up...I am guessing quite a while. Then, the trial itself...what, years? Video footage coming out of the mob busting through, chanting Kill Fisk...built in defense, especially with the DA having been complicit in Fisk's activities.
That's a long-ass trial, and he's mayor during it. Do any of you think someone that rich and powerful (as mayor) will face prison time? If so, when? Never mind that this would be the biggest (possibly longest) trial in American history...the Mayor of New York being a gangster.
It's not just, but I can totally understand why the governor might offer a deal that just makes him go away...especially before any information about the CIA operating on native soil comes to light (which we should absolutely assume Fisk has). He's gone, no citizenship, frozen assets, and it's immediate. I can see how they'd want to prioritize the last one.