I wouldn't know how the disaster affected Pierrot, but in the end, whether the company is Japanese or American, it's STILL A BUSINESS. Their goal is not to turn out quality products, but TO MAKE MONEY. Quality is subjective, and more often than not you'll see good quality products not sell well, wheras many mediocore or even bad products often do quite well. Naruto Shippuden has become an example of a series that relies more on its brand name than on qualities like story-telling, animation, acting and music, and so far it seems to be working just fine for them. Why in the world would they up the production values/hire better writers and animators and reduce profits as a result? Some businesses do take special care of their craft, but as a general rule, they will stick to a model that they will feel make them the most money. On top of that, Japanese companies are extremely conservative when it comes to their business models. Once they do something that's making them a lot of money, they stick to it.
While I am disappointed in the adaptation of Naruto thus far, from a business perspective I can't blame them for doing what they do. It seems their customers love Naruto no matter what, so of course they would take the easy way out.