Do ethics guide your shopping?
After sleeping over it, I think I stated my view too timidly. I think the chief ethical principle at stake here is that a community shouldn't punish its members for their private beliefs. (If such punishment became the norm, I as an atheist would be having a very
hard time making a living in America and its predominantly-Christian society.) According to your description, the proprietors' only sin was to hold a private view that contradicts the community's majority opinion. If that's the only basis for a community-wide boycott, I consider such a boycott ethically unacceptable.
How do you decide where to shop?
Convenience, mostly. But to the extent that ethics do influence my shopping, it's about the consequences of actions, not about rewarding conformism with my personal views. In the case of your farmer, the consequences
of shopping at his store would be that the environment gets protected by consuming local crops; that my community's historic heritage, as embodied in this farm, gets preserved; that more animals get to live in reasonably-happy circumstances rather than factory-farming hell; and so forth. These are all good consequences whatever the farmer believes. I would ignore the proprietors' private belief as long as they don't inflict adverse consequences on anyone.