On my site, a user can control the JS on the page (through some security constraints, not worth explaining the details in the question). Occasionally, they can accidentally create a JS process that will freeze the window as it runs.
Is there anyway a user can click a button, and it will "kill" any actively executing JS functions?
No.
Javascript is single threaded, so it can only do one thing at a time. This is exactly why your page is frozen while it's running. You can't handle the press of a button with javascript if the javascript is already running some code.
You should probably rethink your approach so that this scenario isn't even possible, as you seem to searching for a workaround for a serious flaw in the design of your software.
A possible way to solve this is to use Web Workers. These are background processes that can execute in their own thread. They can do intense calculation without blocking the functionality on your page.
They can reload the page. If you keep track of the context your JS is in (with localstorage or cookies), you could reset that context after reloading so it would appear to the user as an interrupt.
