Well to be fair, the dock indicator is on by default. But I'm not griping about efficient hands off app management, in fact that's brilliant. What bugs me is a dirty dock in my spotless OS X on my super clean rMBP. If it's efficient for an app to be open after I close it, fantastic. But I'd like for the indicator light to not loiter around on my beautiful screen for apps that don't have any windows open.
You're right, if an app is going to always be open then the indicator isn't useful. But it can be useful, for example on an OS where you can have multiple windows of a given app.
So I could rephrase the original question: is there a way (hack/tweak/app) to disable indicator lights for "open" apps that have no windows?
"Just getting used to it" is the philosophy of savages and Windows users. Human progress is the result of intelligent people refusing to "just get used to it". I'm not ashamed of my intelligence, and I embrace my capacity to see room for improvement.
This topic isn't about a gripe or anything whatsoever to do with Windows.
As far as Command-Q, I understand how to quit an application, there are several ways. The question wasn't about how to manually quit an application. Like benwilly said, the brilliance of a modern OS is that it automatically manages what used to be manual tasks—I would like to make it manage the indicator light once it's done indicating useful information to me.