Do you use the Youtube.app at all? Because if you don't use it, you can disable it. Go to Settings > General > Restrictions. There you can disable several apps, one of them being the Youtube application. With the youtube.app disabled a youtube link in Safari will no longer redirect you to the native Youtube.app. The Youtube application icon will also no longer appear on your home screen/springboard and you will not be able to launch it from spotlight either, so you'll need to use the mobile youtube site in Safari if you want to browse through Youtube video's.
If you're not willing to disable the native Youtube application there is no way to change this behavior.