I see both sides of this story. On one side, I can appreciate that it must be immensely frustrating for devs to pour time, effort and money into a project that can then possibly be blocked by Apple on the pickiest and flimsiest basis.
On the other hand though, everyone knows the rules going in. It is inherently risky to base your business on the whims of another company. If you are risk averse, there is Android, and there is the possibility of building stuff in HTML 5 as a web app. No-one is forcing anyone to take the risk on building an iOS app.
The other side of this is that Apple stands to lose ground if devs become wary of investing too much in iOS apps, so it is in everyone's interests to be clear as possible about what is and isn't allowed, and be consistent about it.
And remember, there was huge demand for 3rd-party native apps after the iPhone was launched, but Apple didn't have to even allow them in the first place. Apple made that demand work for them, but (for the most part) made clear rules about what they would and wouldn't allow. I think many reasonable people could have told the makers of AppGratis it was likely to fall foul of App Store rules. They took a gamble anyway. They lost.
Of course there is no reason I can see why AppGratis couldn't return in the form of a web app that is tailored for iOS screens.