The answer to your question is elementary: by charging developers in a usurious way, Apple can get a lot of money and become richer than their competitors.
I fully understand your anger, but in a free market a company should have the freedom to become richer than its competitors. It cannot be the task of the European Commission to cut these normal market mechanisms (and even incentives).
But antitrust law typically centers around leverage a strong position in one market (example in this context: you control and sell the OS) into another one (example in this context: apps). Note that I don't know if the examples I give in this context really work in the sense of the law. It might not be that the first (apple is owner of the OS) is not enough of a market to be a potential subject of regulation.
Playing advocate of the devil to my own tune, Apple didn't get sued for preferential treatment of its own mediaplayers wrt ITunes either. Similar with music market. You could maybe easily substitute the above examples with older Apple markets (or MS with Zune)
OTOH, there people wanted to get entry to a new market, and are not getting kicked out of it as in this case.
It may be more promising, however, to use other ways to express your concerns. You could open an online-petition to Apple. And you could abstain from submitting your software to the App Store (giving a hint on your web site or in the documentation of your software how to make it usable).
The purpose of your petition could be to request Apple to either open the GateKeeper to signatures of third-party authorities (which are more expensive than the costs of the Apple Developer Program, however) or to keep the behaviour as it is in Leopard, Snow Leopard or Lion, i.e. informing the user that the program has an unknown source, but letting him or her the choice (without changing the system's preferences).
I doubt that will work. They knew it would cause an outrage, they did it anyway. Only something fairly major will make them change course, and no, I don't think some media noise in OSS circles will do much.
It will have to be something like an antitrust investigation, or a Vista like user revolt. But I don't consider the chances on that very high, most of the press is consumer oriented and currently cheerleading every move Apple makes. And in Apple's case there is no through more business oriented press, like there was with MS.
It will be a long road, and without Apple coming down from its current cloud (pun intended) will make them flexible and actually simply need 3rd party programmers again, nothing will happen. And, if the previous situation is anything to go by, that can take a very, very long time.