Instead, Scientology appears to have largely ignored Burroughs' criticisms since he left, their only visible response being a reply to one review in Rolling Stone (their letter was reprinted in Burroughs' Naked Scientology). (This lack of reaction is itself unusual, suggesting that Burroughs failed to come to Hubbard's personal attention as the latter was just starting the Sea Org.)
Hmm... Seems like someone is writing without first researching. Burroughs was well known by the Church, who touted him as an "internationally famous author" when he was cleared, and then later followed his criticisms enough that they responded. Granted, they didn't resort to R2-45 (killing him) or any other harsh methods (beyond declaring him in a Condition of Treason and kicking him out of the organization), but they certainly took the bait; they engaged him in dialogue. Mary Sue and L. Ron Hubbard both penned replies for Mayfair, with Hubbard going as far as to call Burroughs a friend.
The scathing tone of the above link is unwarranted, I feel. There was a vagueness in Miles' words that allowed for the interpretation that he wholeheartedly believe in Burroughs' success in this particular endeavor, but I feel the author is being unreasonable. Moreover, they start by saying it's a "minor annoyance" and end up sounding genuinely exasperated.