Where does your 99% number come from in "Windows scare away 99% of users from running the installer"?
From what I've seen, on the contrary most non-tech users simply click on "accept the risk" every single time there's one of those "scary" screens. They just do, just like they bypass HTTPS warnings in browsers. After all, most informed users us included do the same, maybe after a 5-10s pause in front of the screen to read the company name.
The number of people "scared away" seems way less than 50%, and I'd imagine it is probably around or even less than 15%.