Well, Microsoft is locking down Windows 8 pretty hard, too. First with UEFI, then with the Windows 8 store where they'll only let you install apps from the market in "tile mode" and they'll even be able to remove apps from your PC. I know they still allow you to do everything in the non-tile mode now, but what happens when they remove that mode in the future?
How long will it be until RIAA tells Congress that "Microsoft is not doing enough to stop piracy (even though they have the capability)", just like they are doing now with Google, and then gets them to remove "unlicensed" songs from your PC?
I think stores are fine. They are a pretty good way to show you the best apps for the platform, and they also help a bit with safety, but they should still allow you to download and install whatever you want from the Internet if you choose to.
Android has a pretty good model here. They have the Market, and then if you really want to, you can get apps from other sources, too. Although, I don't think they should even ask you if you want to "enable 3rd party sources" in Settings. It should be enabled by default, and maybe just give you a warning whenever you want to download a 3rd party app, just like they do in Chrome.
The point is I don't want to lose any of the freedoms of what I can do with my computer, just for the sake of having a store that streamlines app discovery and makes me safer when I use it. I should have both.