They didn't stop him. Haven't you said that they acknowledged that under Nord law he had the right of it so the duel went on? Something in one of your quotes about how the King couldn't refuse the challenge without losing face...
I don't doubt the Imperials would want to arrest him, and might even do it, but with the king's own courtiers having approved of the duel the arrest would seem a very bad idea. Everyone there would be called to answer for why they let it happen, and have to say 'it is Nord law'...in the face of that practically every Nord (including the ones in the legions) would be calling for his release (obvious exception being the not so merry widow), and executing him would mean a united Skyrim screaming to secede and mass desertions from the legions...probably even outside Skyrim, where the legions have a large number of Nords in the ranks I think. If Ulfric wanted a united and independent Skyrim getting arrested may have been his best available move...and certainly would have saved poor old Roggvir.
But that's a different game. A Nord war of secession would have been very cool. Would have required near doubling of the world space and I don't know if it would have been that much cooler than the civil war they opted for though, so the design choice is certainly understandable.