No, you're right. But the other thing is that Gatekeeper isn't intended to keep OS X secure. It's intended to make running non-Apple code annoying and nothing more.
To do that, it would have to be combined with making getting software from the Mac App Store, most of which is "non-Apple code", annoying. Presumably, then, you're saying that getting software from the Mac App Store is annoying.
Or perhaps you meant "it's intended to make non-Apple-approved code annoying", where "Apple-approved" means "approved by Apple to go into the Mac App Store". Whether that's the intent, yes, that's definitely a side-effect.
(I run non-App Store code quite a bit; for code installed by downloading a .dmg or installer package or..., it's a minor nuisance, and for stuff installed by downloading a source tarball, unpacking it, and doing the configure/make/make install dance or whatever that tarball requires, it doesn't come into play at all. At this instance, my biggest peeves with Apple software are 1) dealing with LLDB's misguided attempt to have a "better" command language than GDB and 2) having to teach Yosemite autocorrect that "sshd" isn't a typo for "sushi", "tarball" isn't a typo for "tarsal", etc.. :-))