A few options:
Remove the php include and exit while amending this..
Add your javascript functions to put up the message boxes
(I couldn't say what you need to do to make the modal item work - check the documentation on the plugin)
Note there's no such thing as a jquery enabled browser - jquery is javascript - it's a library of code to make working with javascript easier
So once you have it all working with javascript put back the php and as Dagon points out you need to rethink your logic flow:
if the include runs some other code, conditional on what the actual user status is, then that will run regardless of your javascript
Clearly you should rethink it before doing any rebuilding
Note including another script is not a redirect as such - a redirect is when you bounce the user to a new page or a new script, so while the end result can appear the same, different things are happening
Why not just leave it as it is, forget the modal stuff - show the message on the page via PHP but don't do any exit - then if there is a message to show don't run the next piece of code that you are currently avoiding by doing an exit
(once you have a simpler logic path, adding a javascript solution should be easier)