Not to belittle the JF lovers here, but nobody forced him to do TATV. If he really had a problem with it from the get-go, why did he do it (besides the obvious monetary reason and working again with Sirtis)?
If I had to guess, I'd think that he was just fine with doing it at the time, just like Berman and Braga really thought they were doing something nice for Trek fans at the time, and only in retrospect, like B&B, is he stating that it was a bad idea.
Another possibility:
Braga or Berman called him up and pitched the idea of coming aboard as a "valentine to the fans" to him. It sounded good over the phone. Having known these guys for years, owing much of his career success to Berman, he agrees and signs the contract to guest star.
Then he gets the script and realizes that it just doesn't work the way Berman and Braga wanted it to work, and that it in fact inadvertently ends up disrespecting the ENT cast and their work. But it's too late to back out, because he already signed the contract.
If you sign a contract, you
don't really have a choice. You've got to do it. Otherwise, you face both monetary consequences from the studio, and penalties from the Screen Actor's Guild.