I'm not sure if it's important, but many scholars challenge the authenticity of Muhammad's authorship of that letter.
Then again, most scholars doubt the authorship of Matthew, Mark, Luke, and John, Paul, etc.
Regardless, this letter is generally not considered a firm teaching of Muhammad's. Nevertheless, the Bedouin of the Sinai Peninsula have largely left the monastery alone. I once read ethnographic studies of some of the groups there, but while I remember that they had long let the monastery be, I can't remember if the letter was mentioned as a reason; I don't believe it was.
With things going the way they are in the Sinai, I hope and pray that the monastery continues to "get a pass," whatever the reason.