I'm pretty torn, but I would rather keep the pick. The Mets won't be good this year. At best the returns on this investment would be in 2014 and 2015, the former only if we spend next off-season. So really, I think if that pick is a good college bat, I'd rather have the young protected player for 2015 and beyond than one year of Bourn contributing to a winning team in 2015. Whether our pick pans out is the only argument you can use as Bourn is a proven player. I'm all for adding parts every year, but I would not give up the pick for him.
Pittsburgh/Appel really screwed us on this one. If our pick was top 10 protected, I would definitely say go after Bourn as we would have extra money to sign someone using Stanky's bonus (as other posters have pointed out) to recoup the lost 2nd round pick for Bourn.
So in brief, no if we have to give up a 1st round pick, and yes, if our pick were top 10 protected.