The passenger in question (the praying one) may have told the cabin crew what they were intending to do, and therefore the crew let him get on with it. I have this on board on a fairly regular basis, and I don't have a problem with it. If anyone started praying in such a fashion without "warning", I'd just keep an eye out without making it obvious.
I'm not a religious person myself, but I appreciate that others are. Some like to pray in their seats, some do it on the floor by the galley, some don't pray at all. We're all different.
I'm wondering if these passengers who were so worried, pointed the episode out to the crew? If I was on board as a passenger and something disturbed me (so to speak) about another passenger, whether it was praying, drinking, swearing or other behavours, I would talk to the crew - mainly for reassurance.
Gg