The HOOM certainly has a checkered past, but most of the people I've met who were part of that organization live pretty straightforward, serious, mainstream Orthodox lives.
From what I understand, Fr.Jonah runs a pretty sober monastery, and I've never heard scare stories coming out of there, so that's always a good sign. He has made a point of building close connections with Valaam monastery in Russia, understanding that any monastic institution in the US needs those connections if it is to be healthy. As K notes, not all monasteries can say that.
This article is also one that exaggerates quite a bit to make some serious points. While I've encountered bits and pieces of "Bill" in any number of people (including myself -- a bit of a "crazy convert" myself), I certainly have never encountered him all wrapped up into one caricature.
Fr. Jonah, to my knowledge, was never a member of HOOM, but there was a time when he was something of an innocent dupe for them.
I wish I could say I didn't "know" Bill, but I have met him several times, most times in association with one of that monk Ephraim's cult centers.