Will such a program be a first-class citizen though?

In other words, will the user have a harder time using it than using a QML/HTML5 app? I could see that be if only QML/HTML5 integrate well with the phone interface.

If you mean first-class as in look like an app like came with the phone, then there's no way around using a toolkit that has a familiar theme and behavior. The story is no different than a Linux desktop.