To go through the motions means to make a feeble effort to do something, but in this context they were making a sincere effort to do something
Consider the statement "The notion of it was pure idiocy of course of course, but they had to actually make a sincere effort to do something to keep paranoia at bay and everyone from open hostility.". Is the statement "The notion of it was pure idiocy of course, but they had to go through the motions to keep paranoia at bay and everyone from open hostility." false? Yes/no/unknown