You're right that Patrick McNally would have gone much higher had he been willing to commit to turning pro within a couple years, but that wasn't the case. After meeting with 18 teams prior to the 2010 draft, he fell to Vancouver in the 4th round because he was a high school junior who had his senior season at Milton Prep School to complete before going to Harvard.
As we all know, Mike Gillis values intelligence and character when acquiring players, and so he wasn't too worried about the 5-6 years it would take for McNally to turn pro given the intelligence already evident in McNally and the education he would get at Harvard.
This is his freshman at Harvard, and you have to imagine that when you go to Harvard, you're going there for the degree ahead of the hockey. So I imagine he'll complete his four years prior to turning pro. His father, after all, is an FBI agent, so this is a young man who likely has dreams of being a great NHLer, and a secondary plan for his life when he retires or doesn't make it as a pro.
As a quick update on his performance so far this year at Harvard, McNally has 15 points (4G, 11A) in 14 games, and all four goals have come on the power play. By all accounts, McNally is adapting easily to the college game and was named the ECAC Rookie of the Month in December. Here's an article that discusses McNally's achievement and includes his stats for the year up to the beginning of January:
And here's my own write-up on McNally prior to the season ranking Canucks' prospects: