He was a tragic figure, and would have been the greatest General after Washington, and a great President too, had he not sided with Virginia. Still, he is one of the greatest Generals in American history, and must be recognized as such. Despite his siding with the Confederacy, I have to call him a FF.
Skill as a military commander is something to be respected and even admired, even in generals for bad causes.
However, recognizing Lee's impressive abilities on the battlefield is not enough to qualify him for Freedom Fighter status.
Arlington National Cemetery is a very impressive piece of land, and it's appropriate that it's on Lee's property, considering the sheer number of patriotic young Americans (on both sides) he helped into an early grave.