Exactly like that, you create a file with the same name, overwrite the pre-existing token, and it takes the place of the original in-game.
For the end user, it'll be as simple as unzipping the file in the token folder and clicking "replace all".
It'll go like this:
1. Source for the bestiary is defined. It can be D&D, PF, WHF, whatever has the most comprehensive list of critters. If possible, everything from a single artist, to keep consistency in looks.
2. Vote on token style, i.e. square vs round, and border color.
3. Tokens get distributed amongst each contributor. We'll work only on monsters, not humans. For tokens with pertinent variations (like a dragon that can be white, black, green, etc.), you'll send me the picture, and I'll edit it to get the appropriate hues. Tokens with irrelevant variations, like the ones where it's just the same image but zoomed, will get everything replaced by a single one. Ain't got no time to waste on that kind of shit.
4. After setting a reasonable time-frame, we'll settle on a single online token creator configured to the same parameters, and everyone starts working his backlog (at an easy pace).
5. I gather the results, check that everything's working, zip it, and upload it.