I don't think it's a simple thing to just turn off spritesheets. Spritesheets are always power-of-two sized, and while WebGL 2+ supports non-power-of-two texture sizes, WebGL 1 does not. There's still enough WebGL 1 systems out there that I think if it just exported a bunch of non-power-of-two individal images then your game will be broken on a small percentage of systems, but enough that you'll get a lot of "game doesn't work" reports.
Then there's other issues like larger games losing the benefits of spritesheets could become significantly larger to download and significantly slower to load, and have a runtime performance hit too. It could be a massive deoptimisation for your game that slows things down even for players who don't want to mod anything and just play the stock game, which I think is an unfortunate trade-off.
Perhaps some of that can be mitigated in various ways, but it's complicated. Modding is a very large area if you want to go further to adding new kinds of objects, changing game logic, adding new kinds of level themes, etc. as well. I fear this may be one of these areas people say "just add A!" then "just add B!" then "just add C!" and then on for another 20 things over months/years.
Perhaps there's other ways to solve this - for example if Construct could export metadata about spritesheets (i.e. the location and size of every image), then in theory some external tool could take a folder of individual image files and paste them over spritesheets, and that could be robust against future changes to the project. It would keep the benefits of spritesheets and only need a minor change to Construct, exporting some extra info it already has.