I don't think Marluxia was ever in Xemnas' inner circle like Xigbar and Saix were. Xemnas knew he was going to stage a coup which is why he sent away the untrustworthy members to Castle Oblivion. I don't think Xemnas would have done this if he considered him trustworthy enough to reveal the Organisation's true motive. So I understand that he wasn't in on anything, and ended up being his own downfall by attempting a powergrab.
As for this current Marluxia we're seeing, it's possible that he is currently Xehanort's vessel and they didn't want to spoil it by giving him gold eyes for now. Or he has another agenda again independent from Xehanort.