First off, I thought Avatar was a great entertaining movie. It wasn't incredibly realistic and the story was a rehash of the same story we have heard so many times, yet still entertaining. That said, while the movie has a few realism problems I find your argument a bit silly.
You missed a few important details and possibilities.
- The humans came to Pandora not with the goal of wiping out the Na'vi, but with just digging some rocks out of the ground. Some military was sent along to encourage the locals to cooperate, but the original mission was not anything like "destroy worldtree".
- As you have shown, it's a very long round-trip. After deciding to attack the Na'vi, it's not like the humans can run back to earth and grab the big guns, they had to use what was available.
- Your basic premise "well if we have fast spaceships we must have amazing laser guns too" isn't really a valid argument. look at the past 50 years, computers and technology have made amazing leaps and bounds, but we still put on pants one leg at a time. Great advancements in spaceflight doesn't automatically mean we would also have equal advancements in weapons.
- The natives used bows and arrows, which couldn't even pierce the armor on the human aircraft without additional velocity. Projectile weapons are plenty enough to kill them and energy weapons could have been considered crazy overkill.
- The humans on Pandora were from a corporation with some hired ex-military mercenaries. Even if earth has developed stronger energy weapons, it's very possible such "WMDs" are limited to the government military, I don't see GM and Ford running around with nuclear bombs so I don't see why a corporation of the future would have free access to the latest and greatest weapons we have developed.
- Long trip, limited energy. Maybe energy weapons just aren't feasible given that the majority of energy collected needs to be used to power the vehicles, mining equipment, life support, and ships.