I think you need to look much broader than ROIs of green roofs alone.  The negative effect on housing affordability will mostly be attributed to constricting housing construction and making so only high-end luxury housing is cost-effective to build. To put it simply and quickly, any sort of restriction on what can be built or any added cost has the effect of reducing construction and thus housing supply.  This is the main driver of unaffordable housing. Cities like San Francisco and Boulder are great examples of this.  They're cities for the rich white elites and minorities can go live elsewhere and suffer long commutes.  It's indirect segregation. 

If you're not familiar with the state of housing construction today, the rising cost of land, labor, materials and regulation has driven the cost of construction up so much that it's almost impossible to build housing which is affordable.  This initiative is just another item on the pile adding to our housing affordability crisis.