What does giving these bees the right to exist actually do?
It does a fair bit, and the rest of your questions imply you might actually already know what it does.However, like any law, some people are going to break it. You cannot stop unwanted behavior completely. That doesn't mean laws aren't effective.
Will this stop pollutants and pesticides that will continue to be used from affecting them?
Not from the ouside, but it will criminalize their use in the area.
Will it stop deforestation as a policy going forward?
Officially, for the area, yes. The article even mentions it mandates reforestation. Unofficially, only time will tell.