If it really is an engineering challenge it needs to be fixed. We're going on 2 years of Mobile Safari having JIT and UIWebView not having it. They can simply make an exception for UIWebViews without making an exception for the rest of the app. I don't know their codebase and it might be really really hard to fix, but I hope it isn't something they've given up on. It cannot continue in perpetuity, as the web cannot continue to evolve if the makers of one of the most popular browsers have given up on speed improvements.
No they can't: part of a process cannot create executable memory while another part cannot. They'd have to move WebKit completely out of process: a huge task as it already does most text drawing.
An interesting alternative would be to enhance the current 'Save to Home Page' feature beyond specifying a manifest of resources and a home page icon. If this was fattened up to allow developers to make something that looked even more like an app but was running Safari (not a UIWebkitView inside a native app), you might have something interesting.