To play devil's advocate, the consequences don't seem so illogical to me. In real life when one commits a range of different serious crimes, one can wind up with the same consequence, time in the pokey, though with different durations. Nor does the successive progress through the stages seem illogical to me; it seems to encourage the children not to act up multiple times in a single day. My son's public school has something very similar, and the children seem well behaved as far as I can tell. I wish that rigid application of disciplinary rules were all we'd had to cope with at my son's school...
(ETA: ... though I can also see how a child with an anxiety disorder such as Pemberly's might not be well-served by any normal disciplinary system at all which could cause anxiety. Such special circumstances of course might warrant an accommodation, but of course they don't mean that discipline is generally inappropriate.)
That said, I really don't like that your son got punished after someone else stole his pencil, and the teacher apparently made no attempt to get to the bottom of it. I think that any disciplinary rules should be predictably and fairly applied, but that rules are fine and generally desirable. They let people know where they stand.
