Wow, this is such an interesting topic; I can't believe nobody's replied to it yet!
I don't think Tolkien's works could ever be called "pro-war," since he's very careful to point out the various horrors of battle and the losses it creates. But I do agree with your point about war sometimes being necessary. It's kind of a strange balance, really.
In the end, I think what Tolkien is disapproving of is modern warfare, like he saw in WWI. All the heroes are fighting an old fashioned war, with swords and bows; it's the enemies that have machines and explosives and trenches, the ones that are destroying the landscape and killing huge numbers of people at a time.