That doesn't make any sense. Let's assume for a second that these people were in potential legal trouble for the reasons you laid out. How does removing Trump from office save them? Pence becomes president, the executive branch is still in Republican hands, and the supposed sting operation to catch them would still be in full effect. Removing Trump stops none of that.
Unless you think Pence is part of the deep state too, this was all just politics as normal.