I feel pretty stupid to ask that, but is it possible to prevent a creature from crewing, by giving it protection from artifacts?
Like when I have a tower of the magistrate out and my opponent trys to Crew his Skysovereign, Consul Flagship.
I don't think so. I'm not a judge, and nowhere near an expert on the rules, but here is why I think it won't work:
tower of the magistrate offers protection from an artifact. Crewing doesn't cause damage. Also, crewing doesn't specifically target the crew-creature, so one cannot argue that the 'protection' from the tower stops targeting.
If you want to stop a crew, you have easier options: tap em. Creatures with summoning sickness can crew because it doesn't specify the "tap" symbol, and that is what summining sickness cares about. But you do need to turn the creature sideways to crew. So just tap the creature instead of giving it protection
lots of cheap ways to do that