I still don't see why he didn't use the mountains in the Hadarac Desert. You can use magic to grow food for the Riders, create fertile fields to raise livestock for the dragons, and create defenses at the peaks of the mountains. With the Eldunari you could make unscalable cliffs. It was already shown that you can make things grow with magic that wouldn't normally survive in that climate. It's isolated enough from all the races, not to mention any attacking army would have to survive for days marching across a freaking desert.
The reason they can't use Vroengard is because there's a lot more magic there than just the radiation left by Thuviel. Since some of that magic was undoubtedly wrought by dragons, or perhaps without the ability to speak, it would be impossible to remove it all using the name of names since not all of it was bound to the ancient language. The remaining magic after the battle on Doru Araeba is substantial, not to mention the radiation has had a century to permeate the entire island. It's created dangerous and unpredictable species, left a myriad of potential traps, not to mention the mysterious people who have already settled there. It's a much bigger job with many more potential dangers than just the radiation left from Galby's death. In Ilirea, they were able to act quickly to contain the radiation before it spread by sealing the citadel, thus making it much easier to deal with. And even though Eragon had plenty of spells to undo afterwards, it's still nothing compared to the magic cast during a battle with harmful intent. Most of Galby's spells in Uru'baen were to protect himself or his followers, not cause horrific deaths and destruction.