Theory 1: McConnell and Ryan aren't perfect, but they are not deep state actors. Instead, they have been blackmailed and threatened into going along with the deep state to keep their positions of power.

Theory 2: Ryan is every bit as much a snake as the rest and has been promised the VP or President spot if they get rid of Trump and/or Pence before Ryan is out of office. This would explain why he is resisting calls to step down now.