Even being a minority shareholder in a corporation does not necessarily imply that the laws of ownership do not apply. Some authorities (e.g. the Kitzur Shulchan Aruch) do not even allow depositing money in a bank with minority Jewish ownership because of the concerns of ribith (usury). (Even those who are lenient in such a case [e.g. the Shoel U'Meishiv] would be strict if the entire partnership is Jewish.) According to the Maharam Schick and the Shu"t Maharshag, the ribith law should depend whether or not the shareholders have limited liability. It seems plausible that this would be their view in the case of dealing in non-kosher as well since the leniency seems to be based on the halachik definition of ownership which should be relevant to both halachos (see http://www.jlaw.com/Articles/ribis6.html).
Perhaps more obviously and directly related are the discussions regarding the community partnership involved in defining a synagogue:
Modern responsa dealing with the corporate status in the eyes of halacha (a topic with ramifications for other areas of Jewish life as well, especially Sabbath observance and ), frequently cite the insight of the renowned Talmudic exegetist Rav Yosef Rosen (Rogatchover Rav). He notes that a Tzibbur (corporate entity) has historically been treated differently than a syndicate of individuals, no matter how numerous. For example, S'micha (laying of hands on a sacrifice prior to slaughter) and T'murah (transference of the sacrificial status of one entity to another) apply only to individuals and not to corporations. However, the Minchas Yitzchak disputes this assertion and maintains that a bank may not collect or pay out interest without benefit of a Heter Iska. He reasons that if individuals retain their statutory rights in a corporate entity (e.g. one is permitted to sell or to bequeath a reserved place in a Shul), surely a Tzibbur never loses its own very personal identity. He notes that a Synagogue congregation conducts the search for Chometz and that it may not pay interest. Evidently corporations are considered as individuals in the eyes of halacha. Rav Pesach Tzvi Frank suggests that although state-owned bank may be exempt from Ribis problems, a privately owned bank is certainly not.
If memory serves (which it well may not), Rav Moshe Feinstein was lenient with regard to loaning money to a corporation because of its limited liability, but not (seemingly) with a Jewish corporation's loaning a private individual. I would think then that he does consider shareholders to be considered actual halachik shutafim (partners) with all the attendant halachos of full ownership, which would then presumably be the case here as well.
Theoretically, one could argue that, even those who are lenient with regard to investing in corporations, presumably agree that a company owned by 3 shutafim does not have any leniency due to each individual's minority status, at least with regard to where they are sharing joint ownership of produce with the expectation that it could be divided up, as in the case of a food cooperative. The counterargument, I suppose, would be that (a la the Shoel U'Meishiv) the original understanding of the cooperative relationship might be one of breira (retroactive ownership) such that everyone only ends up really ever owning (retroactively) what they ultimately walk off with, and therefore the observant Jew never owned the non-kosher to begin with. In fact, this reasoning is presumably much more easily applied to a food-cooperative than to corporate stock, which could mean even those who are strict in the latter case might be lenient in the former.