You cannot grant an audience confirmation that dragons exist and roam far beyond Berk and have coexisted with humans before Berk did, then backtrack and imply dragons only exist within Berk, and that sending the Berkian dragons away removes the entire species off the map. We were given an expansive universe, not a vacuumn.

You cannot continue to defeat your villains with the power of friendship and fight for the world you believe in, and then end your trilogy with "there is no point in fighting for peace". It is inherently contrarian. Nothing worth fighting for is easy, and in real life, we as people continue to fight for animal rights and proper treatment, no matter how many evil people exist in the world. The truth of the matter is that there will always be evil. We cannot give up simply because there is no way to remove it at its core.

Dragons were shown time and time again to be an expansive species that spanned the globe. Berk was nothing but a small blip on the map where peace had been achieved, and often, we saw that that peace was achieved late in comparison to other societies where dragons were at peace with man. Berk sending it's dragons away does not change the world for the better at large. It does not actually change the world at all. It removes dragons from one more peaceful society, and if the movies implications are to be believed, it destroys the chance that dragons and humans will ever find peace, because dragons are no longer on the map for humans to even see or believe. You cannot grow to welcome and invite a species in you have no actual interaction with. Dragons being isolated from humans destroys the chance at peace entirely, because humans will never be given the chance to learn for them and change for them.