If push comes to shove, you could even just put it in a designated subfolder "icon" as a PNG or ICO-filetype and it could be manually used when creating a shortcut or launcher. But I know it can somehow be packed inside an EXE-file, too (the ICO-filetype at least) - but since I haven't coded with Ren'Py myself yet, I can't tell you the exact way to do it. I'm sure it's out there somewhere though and shouldn't be too hard to find.
Thanks for taking this into consideration though! You're a Gem! <3