It's admittedly an oversight in design/communication. The suggestion is made (although note: this and future input about the Launcher's functionality should go into the
Launcher Feedback forum, this has nothing to do with any of the mod packs themselves per se; I've already flagged this so a friendly moderator can relocate it for you, but you may want to note that for the future). How the Launcher Team decides to address it -- if they decide to do so -- is something we'll have to wait for word from them on.
As a side note, running even some installers from desktop have resulted in some horrible folder-spawning messes for me in the past. It's a general rule of thumb (that I occasionally ignore at my own peril) to not throw executables directly into your desktop, but to drop them into a "Downloads" or other such folder. But that's just me, I generally assume too much about people's computing habits and what's obvious (considering I still cringe every time I see my mother go to Google and search for Facebook every time she logs in rather than just going to the domain directly).