Boutique-roasted decaf coffee beans often are more expensive. But the logic also doesn't hold: it assumes coffee is being sold at or near the cost of its material inputs, and that's certainly not true. If you have a reasonable built-in margin for your coffee --- and boutique roasters certainly do --- it can be normal and rational to price irrespective of your cost basis. Customers are brand-loyal (especially if they have to go out of their way to buy your stuff). You want to get them in every packaging they're interested in. All sorts of products are "loss leaders", for that reason, and here we're not even talking about that; we're just talking about something slightly less profitable.

Finally, just a note that the "lower-quality bean" thing is itself sort of hollow, in that: you're probably not buying the absolute best quality means no matter what coffee you buy, even if you're driving to a coffee roaster to get them. Unless you're an extreme coffee weirdo, there is, I'd confidently bet, a higher-quality bean available to you that you're sacrificing because of cost and convenience. Certainly, if you're buying beans of any sort at a supermarket, the "best bean" thing is inoperative.