You've identified a host-named site collection in your environment where application pool isolation has become important. To achieve this level of isolation, you will need to create a new Web application with its own Application pool.

I've created a PowerShell script to illustrate one way of doing this. This script can be downloaded from the TechNet Gallery located here: http://gallery.technet.microsoft.com/office/Migrate-host-named-80d73c79