They also promise in their license agrements that all dot upgrades will be free, now they make a mistake to not making the 3.9 free in MAS. It's a business, and should by so follow business ethics.
CoverSutra also broke many people's promises by having people to pay for a dot upgrade that was pushed to the MAS. I'm pretty sure Sophie and the Agile devs would make it free for existing users, but that's a limitation of the Mac App Store. If you make it free so that existing users can switch to the MAS version, you make it free for everyone else. Companies choose not to do that because it's business. The ultimate goal of every company is to make money. How many people do you think would jump on the bandwagon if version 3.9 was made free? It even includes a free upgrade to version 4. The devs priced it at 50% off for a limited time so that existing users don't have to pay the original fee for the app. Think of it as a normal major upgrade from 3.8 to 3.9 since the upgrade from 3.9 to 4.0 will be free.
Imagine all the people who see that 1Password was free in the MAS for a limited period of time, be it one day or one week. It's a popular enough app to bring it to the number one spot in the store if it were free. Even now at $19.99 it's 3rd on the Top Grossing list (at least it is in the HK store). The sheer volume of new users would flood Agile. The increase in the user base will cause great strain on the team at Agile, they will be spending more hours helping more people. The team needs to be fed, and their method of feeding themselves is making this product. They won't be able to sustain themselves with the costs of hosting and supporting such a large user base where many of them haven't even paid for the product. Think about it from a developer's point of view.
And finally, I'd like to quote the upgrade policy from Agile's site.
Historically, AgileBits has been very generous with upgrades. Your purchase entitles you to free updates until the next major version upgrade. That means if you buy a license for version 2 of a product, you will get all 2.x releases for free, but upgrading to version 3 might require another purchase.
I will agree with your point that it is made clear that all dot upgrades will be free, but again, with 50% off a dot upgrade that also entitles you to a free major upgrade doesn't sound too bad does it? Also, I would think that the changes in the 3.9 version would warrant it a borderline major upgrade.