It's an underlying vulnerability with the game. They'd still have to send files back and forth to the installed app, and that can still be injected with the malicious files. You just wouldn't be typing into the console. Unless they also built an anti-cheat client into the game, there would be no difference in terms of scripts.
The only advantage an installed version would have is slightly faster loading times due to the images not having to be loaded. For example, your city layout wouldn't be stored locally, but rather sent to you every time you open the game. It is possible that an installed game would allow higher quality graphics (actually real-time rendering of the 3D models instead of the 2D sprites we have now?).
All in all though, I doubt that Inno would kill the browser version, even if they released an installable client. InnoGames is built on browser-based games, moving more towards mobile apps, and they can reach a much wider group of players by their games being accessible through a browser. That's actually one of the main reasons I joined the game, as my old laptop had an iGPU and couldn't handle most games, so I turned to browser games.