1. I agree with your preference for the minority view on the breach of s. 6(1). If you are right that an inchoate appeal to positive/negative rights underpins the majority, I would go further and say that such a classification is both distracting and unhelpful when it comes to analysing many Charter rights (and perhaps any const'l rights). Consider the franchise -- one cannot conceive of exercising a right to vote without considerable state 'intervention' to make it happen. So too with entry to Canada (coincidentally, another right attached to citizenship). The default position of all states that consider sovereignty to reside in the right to control borders is that the border is always already closed unless and until the state assents to entry. And this state practice reaches well beyond the border (as in the title of a 2011 gov't initiative) -- a citizen cannot board a plane for Canada without a passport, and if you pitch up at a land border without one, good luck entering. This is why in Abdelrazik (as I recall) the FC grasped that a right to a passport is encompassed in the right to enter. So there is no zone of freedom within which which [lawful] entry to Canada happens in which one might imagine a negative right to be free of gov't interference in entry to Canada.The factum prepared by the Asper Centre can be found here.
2. The 'floodgates' concern you identify fails to distinguish those impediments to entering Canada that are exclusively within state control (consent to prisoner transfer, border clearance, passport issuance) and those that are not (funding a plane ticket). As it happens, Canadian embassies/high commissions do sometimes pay for flights of Cdns who are stranded abroad for one reason or another (usually catastrophic events outside their control), but it is often a loan, not a gift. In any case, one need not take a position on whether the gov't has a legal obligation to do that in order to dispense with the floodgates argument.
3. If one recognizes (and takes seriously) that withholding consent to a prisoner transfer does violate s. 6, the discretionary criteria in s. 10 are not so 'evidently pertinent' after all. If I am a citizen, why does it matter how long I have been absent, whether I have family members, what my intentions were in leaving or remaining outside Canada, my health status etc.? The point of being a citizen (as opposed to a permanent resident) is that these things don't matter. I cannot see how the fact that I'm a prisoner seeking transfer transforms them into justifications for a denial of my s. 6 right, unless one implicitly downgrades the right to a privilege. The only plausible contenders for justified grounds to limit the right are those that relate to security/public safety. This is what the FCA's fanciful hypothetical was about. Yet even this is ultimately irrational: It relies on the notion that a person in a Canadian prison poses a risk to public safety/security. In other words, it asks us to accept that Corrections Canada cannot protect Canadians from offenders while those offenders are INSIDE prison, even though the detaining state seems able to do so, and Canada seems able to do so with respect to all the dangerous people already in Canadian prisons. (The Federal Court's fanciful hypothetical tried to maneouvre around this). Indeed, if a Canadian is convicted in Canada, Canada simply has no choice but to find a way to incarcerate that person and keep everyone safe. So it is neither rational nor plausible to claim that the same can't be done with a Canadian incarcerated abroad. That is, there is no justification once one genuinely recognizes that the right of a citizen to enter is breached by withholding consent to a transfer. I suppose one could try to make something out of the cost considerations of incarcerating Canadians transferred from abroad, but this seems pretty lame and, in any case, it ignores the reciprocity upon which prisoner transfer is based -- Canadians are transferred into Canadian prisons, but foreign nationals are also transferred out.
Any further thoughts or comments are welcome!