If I were the secretary of the UN, and a corporation whose fundings exceeds that of several nations, and that employs people such as Lovecraft (Inventor of the Dark dreamer project, which became the avatar project) wanted to design a spaceship with weapon capabilities and equip it with nukes, and send that to an alien planet, of which the only intelligent live lies on stone age levels, I'd sure as hell withdraw that mining license* and dismantle the compagny if I could.
The first mission to Pandora was done at great expense, using a 4 km ship. Considering the enormous energy costs involved, there would be no space for redundant features such as weaponry. After that they knew about the Na'vi, and using nukes and orbital weaponry against stone age people seems a bit redundant, doesn't it. Especially when you are having serious PR problems already, and your ship only has a 350 metric tonnes of cargo capacity. (Which isn't a lot on astronomical scales, believe me)
*The RDA was only permitted the right to mine the planet after PETA screwed up their campaign. Turns out using a human with implants as Na' Vi was a bad idea.
Last but not Least:
THERE IS NO FTL TRAVEL IN AVATAR (0.7 c is fast, but not FTL)
The only star they can reach is alpha Centauri, and that only at great expense. All power generation is done by fusion (excepts for the ships main drive, which is an antimatter/matter reactor). Unlike fission, fusion can not be brought to explode. Besides, since fission is barely used anymore, the amount of nuclear weapons would most likely be less, not more. Antimatter/matter reactors being as dangerous as they are, I expect them to be strongly guarded. The deuterium and he 3 required for fusionpower on Pandora are gathered from the gas giant around which the ship flies, using retired shuttles.