This has disaster written all over it.
For the government, sticking with the project likely means having to explain to the public and the Air Force in 2016 why the latter must find a way of extending the operational life of the CF-18 into the 2020s. When the Air Force responds by grounding the fleet of CF-18s because they are no long safe to fly, then the government of the day will have to explain to the public why Canada is like New Zealand, and doesn't really need a combat air force anyway.
For the Air Force, selecting the F-35 on whatever paper rationale the sky-nerds at NGFC came up with was an error and they might as well have suggested that the government order X-wings. At some point soon a competent leader in the Air Staff really should call bullshit and tell the government that whatever it looks like on paper, the F-35 is a fantasy and likely to remain so for many years, thus an alternative ought to be procured.