Yes but that was Xemnas, namine has the power to create actual (though false) memories from nothing. Theoretically she could've recreated the missing ones from nothing. (after examining what to copy from Roxas)
And wasn't it technically Namines fault the mess started? After all Xion was created before sora's memories were tampered with and both he and roxas were just fine.
It wasn't until Namine started messing around that everything went all to hell so to speak. xD
However, to do that she would still need to untangle both Xion's and Roxas' own memories in order to find those who are Sora's, then examine them and do something with them.
The problem was not that it was "impossible" to restore Sora without having Roxas and Xion disappear at first, but that it would take far too long. If Riku, Naminé and DiZ had chosen that approach the Organisation would have reached their goals already. It was practically a race against time. Also, the longer this whole mess played out, the more complicated it would get due to Xion's leeching ability and Roxas being used as an "intermediary" to catch Sora's drifting memories.
Days said:
Naminé: But if they join with her memories, things get a lot more complicated.
I would need to untangle her memory before I could finish Sora's... What was
supposed to take months might take years. DiZ would be furious.
Riku: So what's the solution?
Naminé: If I try to just jump in and rearrange her memory...then I risk Sora
waking up to find out that nobody remembers him anymore. I can't do that to
him. It's too late either way. His awakening will have to be delayed. I never
imagined Sora's Nobody and the other one would fight so hard to be their own
people. Unfortunately, the only real solution...is for them both to go away.
Naminé: Did you know her face was blank at first? Only now can you see
someone. That proves some of Sora's memories are inside her. Some inside
her, some inside Sora...others inside Sora's Nobody... I can't sort it out
anymore. All I can do is pick up the pieces once what has to be done, is done.
By the time the above conversation happens (Day 276), the mess has become already so heavy and confusing that even Naminé herself lost track of how and where to look for Sora's specific memories ("I can't sort it out anymore").
Not to mention by this time both Xion and Roxas have created so many memories of their own that searching for those of Sora inside them would be an arduous task that, coupled with Xion's natural leeching ability and Xemnas' scheming, would take far too long with no guaranteed success, that's why Naminé proposes the only "real solution" that is now left for them to take, despite being uneasy with it.
It was technically Naminé's fault all this mess started, yes (and that's actually what makes me shiver everytime someone feels the need to ship her with Roxas, she not only brainwashed him but also caused his disappearance), but when looking at the whole picture she was forced into it by the Organisation, and thus by extent by Xehanort to do it.
The original plan of Castle Oblivion was to use Naminé's power to turn Sora into a puppet so that the Organisation could have used both a Replica copy and Sora to collect hearts (the Replica program was started before Roxas came into the picture), and later both Roxas and Sora. However, Marluxia hijacked the plan and so Xemnas turned to using either both the Replica and Roxas or only one of them, whatever worked best. So, in the very end, Xehanort and his plans are the culprits that are responsible for not only TAV's, but also Roxas', Xion's and Naminé's suffering.
All leads back to Xehanort directly or indirectly as the cause of things.
Nomura actually goes into detail about this in the Days Ultimania (which is actually something I feel that should have been included in the game Days from the beginning):
358/2 Days Ultimania said:
-- The "Replica Plan" that was the key to this game, was it begun with Roxas' entry into the Organisation?
Nomura: No, earlier than that. Originally Vexen was working privately to advance the research on Replicas, but for the Organisation's goal of completing "Kingdom Hearts of people's hearts" they needed to use the Keyblade to recover hearts, so they switched to this plan of copying the Keyblade hero. As for who was or wasn't told about the "Replica Plan", that depended only on their different missions.
-- So at the start of the Replica Project they didn't have plans to get rid of Roxas?Nomura: That's right. Originally the plan was to keep their power in balance. If it had been maintained, there would have been no need to get rid of one of them. But in the end Xion began absorbing too much power, and so they no longer needed Roxas. Xemnas had nothing to do with the plan, however, and only the people below him were concerned with it. Xemnas only cared that Kingdom Hearts be completed. Originally the Castle Oblivion plan was to use both Roxas and Sora, but since that changed it would be equally convenient to wait until Sora woke up in Kingdom Hearts II and use him then.