Who owns the building? MIT or the personnel of CSAIL? If the building's owner wants a log of who came in and out of the building is that really something Mr Stallman has the power to object to?
My guess is that, in this case, nobody at a high level made a decision in the first place, but rather a mid-level organization like MIT security or facilities management instituted the policy. Since they probably are delegated responsibility over building-access systems, they can do that. But the building inhabitants can also try to complain about the way their departments' buildings are being managed. If you were to ask more specifically, "does facilities management or CSAIL own the building?", the answer is sort-of neither, and sort-of both: it's owned by the corporate parent of both of them.
What if MIT were logging who went to the bathroom?
There's clearly no fundamental difference in securing a different part of the building. Does Mr Stallman (or perhaps an employee of the building if he's just a third party) not have a basis to criticize MITs tracking of bathroom habits because he (or they) don't own the building?
In what way is door access different?
Stallman's thesis is "logs have no use". I'm sure the building's owners disagree. Let's think of a possible use-case:
"Someone stole a laptop from Room 214 over the weekend"
Do you honestly think someone who wants to steal a computer will use their own access card?
Tailgating through doors is a lot harder when everybody knows that the doors log everything.
Indicating to MIT professors that they can't be trusted to use the bathroom responsibly is stupid because the consequences of "bathroom abuse" are very low - hell, who knows how many Nobel-prize-winning ideas were developed on the toilet. Further, they're not being paid to be present and take calls/help customers/make widgets. They're being paid to produce research findings. So even if they are spending all day in the bathrooms, as long as they're publishing, who cares?
Think about it like your house. I'll happily have keys made for extended family and close friends who are staying over. I know them, we will have an ongoing positive relationship, and I trust them. But what about the cleaning service? What about contractors? What about Airbnb guests? Given a checkbox, I'd definitely choose to log their entires. I probably wouldn't read the logs, but I'd feel better knowing they existed.
Before you say NSA, I'm collecting data on my house, not all the other houses on the block. I get to do that. There is no right to enter my house without letting met know about it.
This is MIT's house.