The deep state thrives because the middle managers think they're safe. If you just prosecute the guys at the top they will just be replaced and the same middle guys will serve the new overlords just as well.
But, if you start throwing the middle management in prison for 20 years for "just following orders", then nobody will be willing to stick their necks out for the next batch of overlords.
So, start prosecuting, and publicizing, mid level bureaucrats for their roles in all of this. "Joe Schmoe analyst from Langley was just sentenced to 20 years for his role in the Obama gate scheme" will have a lot more impact than 5 years if back and forth about how far Obama's immunity goes.
Even if you can't bring criminal charges, imagine what happens when "50 former intelligence officers" all lose their houses to Trump in a libel suit.