That depends, the civil service has a lot of leverage because most of them cannot easily be fired. And POTUS needs the civil service to execute his policy goals so his fellow party members and possibly himself can get re-elected.

Therefore there is considerable leverage for allied servants to form an alliance that more or less offers their allegiance in exchange for non-prosecution. I would expect especially DHS to basically become a non-functional (or even seditious) department if they prosecute those guys and they could purposefully make the president look bad by making his security apparatus look incompetent.