Friendly Atheist has a post on the California Ashtanga yoga story, too, with quite a few comments. There is a good deal of debate there over whether yoga must be taught with spiritual/superstitious components. However, the real point is that this class is being funded by the Jois Foundation, whose website is here. There is a good deal of pseudoscientific, superstitious info on that page, including some details about how yoga somehow generates "internal heat" which burns up "impurities in the body." Most atheists would, I suspect, be dismayed to see any class being taught by a Christian group that had such blatant pseudoscience on its website.
So, does this mean the classes as taught in California are unquestionably religious in nature, and thus unconstitutional? No. We don't have enough data to know exactly what's being taught there. I do think, however, that we have adequate information to understand the concern of the parents who are complaining and threatening legal action. A simple web search shows that this particular form of yoga does have some superstitious underpinnings, and most atheists wouldn't take the word of the school district that all religious aspects had been removed if it were a Christian group teaching the class. As a result, I honestly don't feel that these particular parents in this particular situation should be mocked.