Will terrorism increase or decrease over the next 1000 years? How will people in 3000 deal with dissident political groups to minimize terrorism?

As long as there is fanaticism in the world, no matter what type of fanaticism, there will always be war. Not just terrorism.

Terrorism is a tool of war.

This goes back to the Egyptian and Samaritan times of 4,000 BCE and respective slaveries of each other and others.

No resolution of this fanaticism will be the end of humanity.

There simply won't be the resources available on this world to continue the fanaticism.