I think Bryson's putter was center shafted and though I think the lie angle of the club was technically within the rules, the sole of the putter was angled so that it could be soled at > 79 degree angle, which was how he was using it. I think that's why the club was ruled non-conforming.
As far as leaving the pin in -- the Tour could always maintain the current rule. I don't think they will, but they could. In the meantime, perhaps some of the tour stops where low scores are encouraged could coat the sticks with balata to reduce the rebound effect.