I don't see what the big deal is. People are acting like she is the only one who is doing this, but Pixelmator and many other apps are doing the exact same thing. This is just a small $5 app, where Pixelmator is $29.
Seriously people act like when developers say, "Free upgrades until version X" that it is somehow a promise. There is no developer I can think of that actually said, "We promise your upgrades will be free until version X." Sure it is a tacit promise in a way still, and what is being done clearly is making a few people understandably upset.
A year from now nobody will even remember. They will all have their favorite apps bought off the App Store and not even think twice about the developers who decided to drop using Kagi and other e-commerce because of the cost/overhead to support serials and anti-piracy. The developers will be happier, and the customers will be happier.
Go ahead and boycott your favorite apps because they don't have the ability/time to sustain two channels for their app development, but you are only hurting developers who are working hard to make great apps.
It's not like Sophia or the Pixelmator team came up with some grand plan to screw over people and make a quick buck. They clearly thought this over for quite awhile, and considered the pros and cons. The result is that the App Store is the future, love it or hate it.