To me at least, the red lightsaber emphasizes that Anakin is set on his path to darkness and, in Obi-Wan's opinion, cannot be removed from it. He can only be incapacitated/killed, which Obi-Wan fails at. I suppose it does go against the "brother vs brother" theme, but it actually could end up making Obi-Wan look sympathetic since he's attacking someone genuinely twisted and evil. It also happens to appeal to classic imagery (blue vs red) from the OT.

I always assumed this would be in the final edit. Is that no longer true?