Jean's mutation is to become Phoenix. She's always Jean and she's always Phoenix. Besides this stunt took skill and know how, skills that even Charles didn't have since he didn't even think this was possible. Even before splitting it and putting it back together, Jean stored his entire conciousness and mind within her own mind. Not the first time she's done total mind transfers either. She's transfered her entire counciousness into another body before as well way back in 1992. Jean's an OMEGA mutant for a reason.
That's like saying Wolverine never really slashes anything or uses his fighting skills because his metal claws came later.
Jean didn't know Cassandra switched bodies with Xavier because she being his twin, shares a very similar psionic signature with him. Plus, Jean doesn't go scanning people's minds constantly and needlessly unless she had reason to. She had no reason to in Cassandra's/Xavier's case...until the Beast beating occured. Which necessitated that she read Beast's mind without his permission and found out. Jean's incredibly powerful, not omniscient. She's tempers that power with her human passion and compassion, and along with that human fallacies as well....and that's one of the reasons why she's my favorite character.
And once she did find out she did mop the floor with Cassandra in more ways than one. Not only was she able to change her perception to "see" like Cassandra was and undermine her plans from a strategic stand point, I'd say ripping her essence out of Xavier and leaving Cassandra a bodilyless mess more than constitutes moping the floor with someone.