Is the Supreme Court of Canada Decision in Agraira Consistent with the Halifax Citadel Case?

I have posted previously on the recent Supreme Court of Canada decision in Agraira v. Canada (Public Safety and Emergency Preparedness), 2013 SCC 36.

One of the interesting aspects of the decision is the giving of deference to a ministerial interpretation of law, even though the interpretation was only "implied".

How does one square this conclusion (sensible, in my view) with last year's decision in Halifax (Regional Municipality) v. Canada (Public Works and Government Services), 2012 SCC 29, [2012] 2 SCR 108?