Although, it does seem like they could get more granular in app approval, which I am sure iOS devs would not like, but users would. For example, "If your app's primary use case is navigation of the open web, you may use WebView to handle 3rd party links. However, if that is not the primary purpose of your app, web links must open in iOS."
Either that, or give me a setting for each app, which the dev can set the default on. "Open links in Safari."