There were already areas that are out-of-limits for the scooters-by-hour, so I presume it uses a similar mechanism. I'm guessing it would be similar to the letting go of the accelerator, so relatively smooth way to stop it.
I agree that you don't need homophobia to explain this—it could be just any kind of new painting in the area to be an invitation for some people to mess up with it. Lime probably feels that they don't want their vehicles to attract this kind of publicity.
The article claims the new paintings were clearly marked, though the pictures don't seem to show it. Nevertheless, I imagine it is a valid concern for any kind of new road painting that people will mess with it before it's dry (usually accidentally), so they are somehow marked that way to limit traffic. Maybe it was the case here as well, but some people chose to do it regardless.