1. I'm sure this hurts local gaming stores. Its true that a physical copy is not the same product as a pdf, and therefore pdfs are not in complete, 100% zero sum competition with hard copy books. But they are in SOME competition. There is SOME trade off. I personally suspect that the trade off is significant, but that has a lot to do with the fact that I am, as we speak, gleefully saving money by purchasing a DDI subscription and absolutely zero hard cover WotC products. For my wallet, the trade off is 100%.
2. But Paizo doesn't have an obligation to support local gaming stores. Local gaming stores are businesses, not charities or ethical causes.
3. Whether this will, or should, cause gaming stores to not promote Pathfinder depends less on the price of this particular product than it does on the likelihood of selling future products. If this is the first part of a trend of significantly lower prices for pdfs than for hard cover books, I would be nervous as a gaming store owner about recommending Pathfinder to people. I'd market products I was more confident that I'd personally be able to sell in the future. If this is NOT part of a trend, then I might not care.
4. Whether Paizo should care if gaming stores care (got that?) depends on whether the lost revenue through the loss of active promotion by gaming store owners is outweighed by the advantages of selling direct pdfs over indirectly selling physical products. The first has much lower overhead than the second, and in any case many gaming stores are notoriously bad at promoting rpgs. So maybe not much is being lost.
Its all business. For everyone involved, its all business. Some fans will no doubt make purchases based on perceived ethical concerns (support for cheap online pdf sales is an ethical plus to some people for reasons I don't entirely understand, support for local gaming stores is an ethical plus for others for reasons I understand but do not share), but the true victors in this matter will be those companies who successfully exploit for profit these ethical stances amongst their consumer base.