This is almost like hiring an off-duty police officer from your local police department to protect you from corrupt local police department.
The argument isn't take the site offline, it's to not use infrastructure that is openly recognized as being subservient to the same adversary the site's authors are trying to protect people from.
I am also less worried about some random NSA analyst going rogue to come after me. If the NSA is going to abuse its power, it is probably going to be as a whole institution. But some local cop breaking the law because he has a hair up his ass about someone happens literally every day.