He still actively helped Corypheus though. You find a document that says Lucius (the real Lucius) sold out the Seekers to Corypheus, but he ended up not having use for them since they were resistant to the red lyrium.
Was Lucius even the Templar leader? His rank was Lord-Seeker, not Knight-Commander.
Lucius was the Templar leader post-Conclave by virtue of stepping into the power vacuum that was left when the senior Knight Commanders, Templar negotiators, and other leaders were killed in the decapitation strike. Lucius and his cabal stepped in, led the Templars to Therinfall, and proceeded to imprison/brainwash/red lyrium addict the other senior surviving Templars as part of their conspiracy to corrupt the Templars from the top-down.
Lucius wasn't the Templar leader officially, not in the way that Fiona was recognized as Grand Enchanter. He was just a trusted senior survivor of who happened not to be at the Conclave. He led the Seekers, who by and large had helped lead the Templars to break away, which was enough.