I'm getting more and more confident about my earlier theory being true: Finch is waiting to find something to abuse in Samaritan's code, and is going to use the Machine as a weapon to destroy it. After the mess in QSD, maybe Finch finally realizes that ASIs are more of a detriment than a saviour to people. Get rid of two ASIs, maybe sacrifice himself to protect his allies to ensure the program executes, and the world will never know what happened.
The Samaritan/Machine fusion is starting to sound more lofty than an actual end result. Samaritan may have the power and technology, but Finch has never wanted his ASI to be more intrusive than simply reading NSA feeds (which is why he abused the Amendment loophole: built the Machine so tightly that no one can know what it's doing except for Admin. You can't charge him for invasion of privacy at a massive level if no one knows what the Machine is doing).