Add root barrier layers underneath the soil on top of the roof, and weed out tree species known to cause trouble..

See for instance https://en.wikipedia.org/wiki/Green_roof

Significant soil depth can be part of the solution, which no doubt requires additional strength in the structure underneath the roof..

For a worked example:

"The 5.4-acre green roof has soil depths that vary from 18 inches to 4.5 ft. This layered planting system is a structurally engineered component of the building that functions to balance seismic shifting, collect and filter stormwater, and irrigate the gardens. Geosynthetic fill was used to build up the rolling topography of the park while adding minimal weight to the structure."

From https://www.landscapeperformance.org/case-study-briefs/sales... under the "sustainable features" tab.

Just to be clear – my comment was a joke.