The penalty is legit, but it never had to come to that. If he (Payton) didn't try to show everyone that he was the most clever man in the NFL, he could have just run the clock down to twenty seconds or so, leaving the Rams with a much reduced chance at the comeback, Legatron or no Legatron.
The flag flying or not flying doesn't change the fact that Payton was still an idiot that has only been let off the hook on the situation because of this very public non-call. If Nickell had showed up on time - only a split second later - it's a pick or an incomplete pass, and we make the comeback sung to a delightful tune of "what an idiot was Asshole Face". The play saved his reputation.
Frankly I still want to go back in time one step further and yell at Joyner to just knock the damned ball down instead of waiting like a bystander for it to come to him on a horrible pass by Brees. If he had just done his freaking job none of this would have happened. Joyner also got a free pass because of the game's final result.