If you have deployed your silverlight app that is compiled with Silverlight version 3.0.4.0307.0(i.e. Silverlight Beta), your app may work perfectly for the users with Silverlight 3(RTM).
However, if those visitors come across your silverlight app who doesn't have Silverlight installed at all(or maybe lower than Silverlight 3 Beta), they will be prompted to download Silverlight to view your app.
Once they wish to download Silverlight runtime by clicking on the "Get Silverlight" button, visitors will be redirected to Silverlight download location, and the most important part is
*They will get a message explaining that this app is made with Beta version of the Silverlight.
So this may hamper thier experience and impression about your silverlight app and because of this very few people can get to your app correctly *
It is my suggestion that you try to compile your project with Silverlight 3 as early as possible .
Regarding 2nd question What is the possible solution to deploy silverlight website on IIS?
Here is the Answer : You'll need to register the MIME types for xap on your server.