Gonzo is right on target. There is no pressure to participate in noon prayer what so ever. In fact, I was surprised by how many mids chose not to pray.
Coincidentally, I discussed this with the command chaplain at USNA about a week ago. The chaplains at the Academy really aren't too worried about this. He said they hear rumblings from the ACLU every year, and they usually die out. Additionally, (of course this is hearsay), he told me that the former mid quoted in the article wasn't willing to testify, if the suit came to that point.
I can't speak for every recent grad, but I heard stuff about this throughout my academy career, and nothing ever came of it. I wouldn't be surprised if this goes nowhere as well.