I think you are buying in too much to the city's legal arguments, which by definition are hyperbolic.
The locations of Pokestops and gyms in Pokémon Go derive from crowd sourced locations used in Ingress, Niantic's earlier AR game. These locations are generally in publicly accessible places. The geofencing on pokestops is also not that tight - there is never really a good reason to stray off of paths in a park to reach a Pokestop. You might have to walk on the grass if the Pokestop were, say, a statue in the middle of a field, but it's a park, that's what you do.
It's worth noting that in cases where pokestops are located in particularly sensitive locations, like inside hospital wards or at church altars, Niantic has indeed de-activated or re-located them.
My main point is, people trampling flowers are acting badly, either that or the flowers are growing in a place where people are allowed to walk ...
The location in question is a public park that's normally quiet, but people decided it was a good area for Pokémon hunting. It's a public park, thats well within their rights. Ita not at all obvious that Niantic CAN do anything in a case like this, nor SHOULD they be expected to.