At present, it is not possible to use deep linking without suffering the Smart banner being injected by Safari on each affected web page.
This makes the experience of users choosing to browse an associated website significantly poorer as they have to see a Smart banner at the top of each page. People know there is an app store and an app – they don't need constantly reminding like it is still 2010.
Anyone know where a relevant plea can be made to Apple to provide an alternative mechanism here as it damages the ethos of being able to simply use a web browser