You could always have your installer use curl
to make a call out to your webpage...
You could just drop the curl program in the temp folder for the install... execute the call to your page and then delete curl from the temp directory. Of course they could block they could block the call with a personal firewall but that is not any different then them blocking your popup. This would be hidden for the most part which is what I think you are looking for.
You could always write a pascal script right in innosetup to do the call utilizing the winhttp library
Or you could just write a vbscript and execute that with the cscript engine to do the same http call.
That should point you to at least 3 different options to do what you need.