Absolutely ridiculous. These students weren't denied a recommendation because they are religious. They were denied recommendations because they reject science. Show me the slightest evidence that Einstein rejected evolution or thought that the universe is 6,000 years old, and I'll admit you have a point.
Einstein believed in a creator (the 6,000 year test is your standard, not the Professors) and that alone is in conflict with the Professors standards. You can not believe in a creator and accept completely the theory of evolution, therefore Einstein would absolutely not get a recommendation letter. The greatest thinkers are usually quite eccentric and skeptical, and to limit those to who fit yours or the professors mold is as closed-minded as any religious fanatic. Nothing 'absolutely ridiculous' about my point, but absolutely dead on.