You're exactly right, global solutions are rarely applied successfully to local problems.
That being said, Canadian membership in the WTO is a function of Canadian governmental action and therefore continues only in so much as Canadian citizens tolerate it. Similarly, the WTO is an enforcement agency, not a legislative body. As such, it enforces treaties that have been ratified by elected governments purportedly in the best interests of their constituents. Canada has negotiated each treaty it has signed, and has considered the implications and outcomes in light of its own national interest, the WTO is a product of Canadian (and international) decision making, not its source.
The entire point of the complaint is to make international trade fair, or at least as fair as possible. In making international trade fair, the WTO works to prevent dramatic shifts in local experiences. By offering tax rebates on the scale mentioned, Canadian provinces directly reduce the cost of doing business in Canada. By the same token then, the cost of doing comparable business elsewhere is increased by the same amount. In effect, companies that chose to work anywhere but Canada are placed at a disadvantage in competing with firms that are located in Canada. The domestic industries in other countries then suffer unless their governments take equal, or greater, legislative moves. In effect, the internal marketing decisions of one state dictate those of all others if they intend to remain competitive. This is not only a direct challenge to the notion of sovereignty and national determinalism, but also privileges those nations which have the social capital to keep up with the Jones. Further, in forcing nations to accommodate industries or risk market instability, unrestrained internal tinkering disturbs the already precarious balance between the needs of citizens and those of corporations. To remain competitive, and retain corporate relevance, states are forced to adapt to the demands of business to a greater extent than to those of individuals.
In effect, the WTO complaint is intended to protect the concerns of locals on an international level. The system is premised on balancing the concerns of communities across the globe, and will at times arrive at decisions that benefit some whilst clearly disadvantaging others. The key is that the system works to create an overall balance across all trade disputes so as to promote a somewhat equal standing for all domestic considerations. It is imperfect, but it's the best way we have to balance vying interests.