I'll take a crack at the why Apple is "taking flak" for this question.
As photographers we understand the need to have an efficient workflow / post processing system. These systems need to evolve to maintain competitiveness (or at least be in the vicinity), with the competition.
As an "Apple guy", if all else is equal, I would prefer to have that workflow in a native Apple application. Therefore, I personally, have always given Apple (and Aperture) the benefit of the doubt. I have given Apple the benefit of the doubt because in the past they have provided leadership and the desire to maintain a product that is (plus or minus) near the competition.
Why would I throw Apple under the bus for this? Quite simple, I have for the past year (two years) been seeing very little leadership from the Aperture team. Adobe haas demonstrated that Lightroom / Photoshop, etc. is the business that they want to be in, building application for professionals and advanced amateurs.
If you analyzed where Adobe is going to be with this software in 3-5 years, it's is my opinion, that they will be at the cutting edge. Where will Apple be with Aperture? I for one have no idea, completely out of the "pro market" is certainly a logical (if not likely) conclusion.
This lack of leadership / direction, call it what you want, forces me to second guess my decision to stick with Aperture. In analysis of this one issue (D4s raw files) Apple is silent, Adobe has put out a message stating the challenges they are facing, what they are doing in an attempt to resolve the issue. Is Adobe laying out a time frame for completion - no, are they over promising - no. But they are communicating and providing leadership. Are Aperture engineers working just as hard? I sure assume that they are, but if this was as important an aspect of their business as it is to Adobe, then they would provide better leadership.
Unfortunately, as I write this, I am coming to what for me is a very logical conclusion - I need to leave Apple (Aperture) for a competitor that takes my photography as serious as I do.
If others a coming to a different conclusion I would be interested to hear that opinion.