One of the points I was trying to get through, and perhaps didn't do a great job of, was that I keep seeing people/apps trying to use HTML and various wrapping frameworks / toolkits to create the look and feel of an iOS app. Even worse, many of these "apps" don't even need to be apps (end of the article).
We went this route too and hoped we could re-use lots of code we already had but, as you say, the right tool for an iOS app is Objective-C. Un-JITed JS inside a wrapped app with a zillion Objective-C stubs using the DOM in a view-like manner its not meant to represent just doesn't do it.
Its not really a question of what you'd prefer to code in (you'll always prefer something familiar) but what delivers the best result for what you're trying to do. In essence we created two real, not test, apps, one using HTML and one using Objective-C. The clear winner was Objective-C in our experience, at this time. Creating a great mobile interface using HTML5 is certainly worth doing and can be done - but I dont think it should be made to look and feel like an app (either in safari or wrapped) since the "not-quite-right" issues just keep piling up, and if you want the look and feel of iOS you should just go native in the first place.
YQL (the Pipes sister product) is more programmer friendly, and also free. Give YQL a go if the Pipes visual UI doesn't work for you (and it has lots of yummy server side JS goodness too).