Unfortunately, no. It seems as if every web site owner out on the Internet has decided to make an app for the iPad. So, when you go to that site, they want you to use your app, no matter how many times you tell them no. It's an advertising gimmick - and, as far as I can tell, there is absolutely no way to get rid of these annoying things.
Just to say - if you ever find a way to stop them from appearing, I'd be willing to know. I hate it when it happens - as you are. But, again, nothing to do but hit the "x" to get rid of it. Sorry.
Marilyn