When discussing anything involving the NCAA, especially regarding ice hockey it seems, one cannot apply normal logic. It simply does not exist.
I don't believe anyone said you "burn" your NCAA eligibility if you are drafted into the NHL. Obviously you do not, as witnessed by the player list VTG posted. However, until last year, any NCAA player in his first year of draft eligibility could not opt into the draft without surrendering his collegiate (amateur) status. That is why Rick DiPietro had to leave college when he opted into the NHL Draft after his first season at BU. This rule also applied to players at the Tier 2, Junior B, prep school or high school levels. In other words, anyone who wanted to play NCAA hockey could not be drafted as an 18-year old. They would automatically be eligible for the next draft, as 19-year olds.
The NCAA constantly revisits this rule and has made some alterations. As of last season the NCAA stated 18-year old incoming players (those who had signed letters of intent to play at a school in subsequent years) could opt into the NHL Draft without affecting their collegiate eligibility. That is why last year's draft had so many quality college and pre-college players taken (Suter et. al from the 1985 birth years along with the 84s from the season before (Parise, Vanek, etc) who could not opt in the year before without being ineligible).
Unfortunately, the NCAA also ruled that if you were already enrolled and playing at a university you could not opt in without being ruled ineligible (see Al Montoya, who fast-tracked high school and enrolled at Michigan as a 17-year old and David Booth, a late '84 at MSU).
That is why players such as AJ Thelen, Wes O'Neill, Adam Pineault, TJ Hensick and Drew Stafford (all first-time NHL Draft eligible already enrolled and playing NCAA hockey) would forfeit their remaining three seasons of college if they were to opt in this year, but other 86s and late 85s like Chris Bourque, Victor Oreskovich and Cory Schneider (playing prep or Tier 2), to name a few, will be taken in this year's draft without affecting them collegiately.
I know this is confusing but hey, it's the NCAA. They like it that way.