Uhm no, to use Sora as a pawn and mess up his memories WAS planned by Xemnas and the Organisation's upper echelons because they originally really wanted to use both Roxas and Sora for Heart collection. Not to mention that without Naminé messing up Sora's memories (and thus untangling them) Xion absorbing the loose memories and copying the power of the Keyblade would not have even been possible to begin with.
Zexion does imply that luring Sora to the Castle was intended as well.
Xemnas did NOT sent Marluxia and co. to the Castle in order to find the chamber of waking, he sent them there because he suspected them being traitors and wanted them eliminated. It was Axel who was tasked with finding the chamber and no one else.
Vexen was sent to the Castle in order to do further work on the Replica program with Lexaeus being there to assist him. Zexion on the other hand was actually reassigned to the Castle by Saix, officially to oversee Vexen's and Lexaeus' work but in reality because Saix wanted him eliminated as well, which Axel eventually did towards the end of CoM.
Marluxia just hijacked Xemnas' original plan and tried to turn Sora into his own puppet rather than one of the Organisation by controlling Naminé.
This is made clear within Days' dialogue and the secret reports:
Note how Xemnas and Saix speak about "Naminé's work" and treat the chamber only as a secondary matter, the plan of luring Sora to the Castle and mess up his memories originates with them, not Marluxia.
Marly is only using the plan to follow his own goals.
Thus, the untangling of Sora's memories was in one way always also Xemnas' goal, hence why if you want to be really specific, the reason (and guilt) for as to why both Xion and Roxas had to eventually disappear to "fix" Sora lies ultimatively with Xemnas and thus Xehanort as well despite Naminé having been the one to actually do the deed.
Except that luring Sora to the castle was part of Xemnas' agenda which Marluxia ultimatively hijacked.
If Xemnas' plans had worked out 100% like he wanted, he would have had three "puppets" (vessels?) to use and collect hearts: Roxas, Xion with the copied powers and memoryless Sora.
That's the main thing of Coded though, it doesn't add unneccessary baggage and huge twists to the story but instead expands on existing concepts and deepens the already established things while still throwing in some light foreshadowing.
It's ironic that people complain about this when that is actually how a true "side game" should work.
Your experience with the already established whole story and mythos gets enriched when you play it, but it strictly isn't needed to understand the core story because later titles (in this case DDD) expand on what Coded hinted about.
In terms of writing quality, Re: Coded beats almost all side games except CoM by a wide margin and characters like Data-Riku, Data-Sora and their interactions with Mickey, Donald and Goofy get fleshed out much better than both the overdone mega-drama Xion show and the "supposed" RAX trio in Days and the great-potential-remaining unaddressed mess that are TAV in BBS.
It makes me sad to say it, especially as someone who likes TAV very much for what they could be, but Sora's and Riku's Data-"clones" are much better fleshed out actual characters that can be distinguished from the other Sora and Riku than both TAV and RAX have to them up to now, showing that a single game can be enough to shape interesting characters if you just handle them right.
