Everyone, including the Jays, knew that long term, they'd lose the trade. The deal was made for the now (now being 2013-15).
In 2013, Syndergaard was pegged to start at class A+. Starting this year, the loss of the trade becomes more and more tangible.
However, this franchise values not going into a season expected to lose 90-100 games because that would mean lower attendance, tv ratings and overall interest in the Blue Jays brand so I firmly believe they went into the 2012 off season with the mindset that they'd improve the team even at the expense of losing trades long term.