stofke... from my experience visitors like these more then pop-ups, since this only appears on entrance and never again. In fact, i have had emails from customers thanking me for the free software.
As for sites linking to you as "virus.." I don't see where you are getting that? Even if a spyder like google indexes your site they will never index anything inside tags... and thats where the code is.
They are probaly getting that from there computer because I had spyware on mine and everytime I went to a website it said download this program now to display this site correctly. I never did but I would amagine it is coming from their comp.