I think the issue has some nuance that most people miss, but on the other hand I also think a lot of that nuance is mostly red herring when it comes to questions on why SE is the way it is today.
Sure, if we grant that the Square side of things took a nose-dive after Sakaguchi left, there's little use denying that Sakaguchi being pushed into leaving is something "he brought on himself" I.E even if Square's development cycles and practices have suffered in his absence, the absence itself could be laid at his feet.
That being said though - Sakaguchi being absent cannot absolve SE of some of their more atrocious actions after his leaving, nor what they were doing up until the point he left - you can't have the quality function of a company rest on a single person.
More to the point though - I think it's possible, and indeed prudent to question the events and necessity surrounding Sakaguchi being made to leave to begin with.
After all, Sakaguchi's business management and creative output is part of the reason Squaresoft made it to the point it could pursue a full feature film to begin with. You'd think that it's unreaslistic to expect a person to always succeed with every project, and that given his track record, the remaining company heads would be more lenient to his failings.
In reality, Sakaguchi was not pushed out because of his failure, nor due to the losses from The Spirits Within - rather it was facilitated as a reaction to Sakaguchi not playing ball with the rest of the company heads as they started kicking the ball around on merging with Enix, and aggressively exploiting the FF IPs with spin-offs.
The fact of the matter is that Sakaguchi was reshuffled out of his leadership position prior to the release of TSW.
In fact, he also registered the trademark for Mistwalker prior to the release of TSW.
Sakaguchi's reshufflement happened shortly after talks of the merger, and the first red Squaresoft financial report prior to the release of FFX.
FFX-2 was proposed as a means to recuperate losses incurred by FFX's expensive development cycle, as a means of enticing Enix back into talks of merging, which at one point, they backed out of due to Squaresoft's financial situation.
Simply put - Sakaguchi did not get reshuffled, nor quit due to TWS. He was already on that path prior to this.
Mandatory reading. Everything here is sourced.
Also, prepare to grow to hate Wada and SE as a result of reading. You have been Chrono Trigger Warned.
http://www.neogaf.com/forum/showthread.php?t=744184
Long story short though - yes, Sakaguchi is partly to blame for putting himself in the spot where Squaresoft had no choice but to force him out.
Point is though, who could blame him?
Squaresoft's remaining leadership showed undue lack of gratitude for his service up until that point, and essentially aggressively started to pursue a company direction and policy that was contrary to everything he believed in regarding the future of the FF franchies, and the future direction of the company.
TWS was just a convenient and happy coincidence that allowed to company to appear justified in cutting off the "dead weight", when in reality the money grubbing, corporatist SE you know today, was already in the making before TWS launched in theaters.
EDIT:
Also, no Lex - Nomura has little to no power in SE. He's not even on SE board of directors. He's constantly being kicked around, loaded with projects he didn't ask for, nor has the power to decline, because he's the face of SE's character designs and has been for ages.
Nomura is not the reason Versus XIII took a long time, nor is he the reason KHIII took a long time. The reason these projects are taking a long time, and the red tape of SE, is, like it always has been, the result of the suits at the top.
Nomura is not one of them.