The same way most other things are proven. Someone in a position of power says "the checkbox was there and we recorded the value, and this was the version of the TOS at the time" under threat of perjury.
You could, say, post a digitally-signed repudiation of the ToS. Or, interesting concept, of all ToS terms to which you explicitly do not agree.
Put that somewhere that, say, Internet Archive would get ahold of it. Among the Archive's revenue-generating services is providing notarized copies of data that it's archived, essentially substantiating someone's claims that material was available online at a given point in time.
Although I'm sure this could be spoofed easily, whatever version control system you're using almost certainly timestamps commits. You could easily bring up the version of the file that existed at the timestamp of the user's account creation date.