Patchbeam is a great tool, i have it on my home computers and it makes life so much easier.
The only downside is that when behind work proxies that i have no control over I remove it as it serves no benefit. Having an option that leaves a registry key so future upgrades remember patchbeam isnt installed would be nice.
Another minor thing is that if patchbeam is uninstalled, when the user uses PA's "Check for New Version" it doesn't do anything.
Prior to patchbeam it would take the user to the Download page. It might be good to put in a prompt suggesting to the user that PB that does the following "X,Y, Z's" is not installed click here to install it or click website to visit download page.
Giving the user an option to install PB wouldn't hurt but could be disabled by admin if required.
If the company i worked for approved the tool and allowed it's connection then i would leave it on as it makes upgrading so easy.