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?
There, the Minister was exercising a power to make payments in lieu of taxes, from which federal buildings located in municipalities are exempt. The exercise of this power is conditioned on an appreciation of the value that would otherwise be appropriate to accord to the building in question. Here, there was a large gap ($1.5m) between the Minister and the municipality on the appropriate value for part of an historic citadel located in Halifax. The Minister arrived at a nominal value on the basis of the restrictions on the site's use, the municipality at a much higher figure based on a comparison with other buildings in the area.

The appeal, the Court noted, was concerned only with the Minister's interpretation of "property value". The decision was struck down as unreasonable, on two grounds. First, the Minister's view paid no regard to the municipality's evaluation, even though the method used by the municipality was common to all Canadian municipalities. Second, the Minister frustrated the purposes and policies of the legislation: the whole point was to allow for payments to municipalities, but to ascribe a nominal value to something clearly covered by the statutory scheme ran counter to the spirit of the law.

Here is my question, in light of Agraira: isn't the Minister entitled to deference on the "implied" interpretation of the legislation hidden in his exercise of discretion? The Court in Halifax Citadel gave no deference to the Minister in determining the purposes and policies of the legislation.

We have two decisions, then, which nominally apply the same standard of review (reasonableness) but which impose seemingly different standards of scrutiny. Can they be reconciled?