There will always be a anti-NCAA and prep school bias in rankings, mock drafts, etc., as long as the vast majority of folks compiling these lists reside north of the border and still believe major junior is the only way to go.
In regards to O'Brien, he isn't your "usual prep-school" player as he also played games for the NTDP team (some of the games were against college competition), all the major US prospect all-star games, he also played for the Cape Cod Whalers in all the major U-18 tournaments. In these, he more then held his own and even starred.
Also, from posted articles - one of the major reasons why he stayed at Thayer Academy (besides it being a top academic private school, that he could benefit from for his entire life...) was that the head coach there is Tony Amonte, who played over 15 years in the NHL, and he could work with him everyday, along with being able to train full-time at a local training facility that many NHL players from the Boston area (and current Bruins) still train at. Amonte played at Thayer as did Jermey Roenick, Ryan Whitney, etc. So, it's not your usual high school set-up.
But, we'll see what the NHL feels about him on draft day.....