As you hint at, Apple generally discourages websites masquerading as native apps via thin shells. See this SO for some discussion:
Does Apple reject "mobile web shell" applications?
For the current app I am working on, I do all my development by serving through Apache and testing in Chrome. I test on device by wrapping the same set of html/cs/js files with Cordova build process and pushing to device. The only reason that wouldn't work for you to is you must have a bunch of server side logic and conditional rendering of your views.
So either you:
1) Just go for it and try to submit a simple native wrapped website and very well may get approved no problem
OR
2) My recommendation is to do a little reworking of your view designs/interactions such as including a native-mobile-app style navbar, etc. so that the experience is more similar to an app than a web site. Then with your new client/app Views, swap out the server side Controller/Model interactions with a Rest/JSON api.
For example, currently you have something like this:
//Server side
class mainController
{
void fooAction()
{
string bar = getModelThatIncludesBar().bar;
...
renderView($bar, 'fooView');
}
}
Instead, more like this:
// Client side, poor mans MVC
bar = useAjaxToGetModelThatIncludesBar().bar; // pretend this is synchronous :)
...
fooViewElementThatNeedsBarData.innerHtml = bar
Edit: I have drastically simplified things here to try to distill it down to the basic two choices I see. Message me or whatever if you want to chat about it.
