That is likely to change. Why should they sell a superior product for less?

Well, if you know your local farmers and buy from them regularly, it doesn't look great if they jack their prices up unnecessarily. They also know that they're competing against the perception that local food is more expensive. In normal times, factory farms can always undercut their prices, so it would make sense for them to use the current situation as an opportunity to get more people to start buying local (due to the prices!) and hope that they will continue to buy local once the prices invert again (due to the quality).

This has held true for literally 4 years. And it's not some niche store - it's a Kroger-owned chain!

Why not?

Because capitalism? Small farmers are already fighting brutal economies of scale.

If they don't want to charge more though?

When their gas prices go up, their equipment goes up, their feed goes up, etc, they won’t have any choice.

Doesn't quite answer the question (of why they should sell at the highest price they can).

Unless you are suggesting that raising prices today is better (normative sense, since you used the word "should") than raising prices when you don't have a choice. In which case, can you explain more your reasoning?

I wonder though, in specifically this instance, if the price of their feed is going down because of how many chickens have been culled or just flat out died from disease.

But yea, if other cost rise, they will need to rise prices.