this sort of experiment is usually short-lived, so i wouldn't worry too much. our most recent school introduced a similar system but with cards - so you had to take a yellow card home, or a red card etc. in the end the staff realised it was causing a lot of problems with self esteem etc and abandoned it.
but agree with others who say support the school - but raise your concerns privately with the head (if this is a whole-school system) or the class teacher (if just his class).
oh, and 'bright but bored' is no excuse. if he's that bright, it's time he learned that follwing the rules, however petty, is pretty much expected until you are of an age to make deliberate anti-establishment moves...
it all sounds a bit sad, but your ds needs to know that you support the school. setting him up with 'school have got it wrong' in y1 is probably not a great idea.
bright but bored needs raising at parent's evening with specifics regarding to appropriate differentiation, not as an add-on to a complaint about how the school handles discipline. (ie 'thick children shouldn't be allowed to behave badly but ds can because he's bright and they aren't stimulating him' - it'd come over all wrong, however much you attempted to explain that you really meant that they weren't engaging their students at an appropriate level, and would lose you mucho credibility points)
so question their discipline methods, but avoid criticising their teaching at this point lol. it's about setting your target.
i think it'll blow over anyway tbh. these fads always do.