Possibly – but more likely, it was just understood that corporal punishment was less useful and less effective with girls regardless of the school they were in.
There could be no comparison for the boys, co-ed schools just followed suit, caning boys in similar numbers to all boys’ schools, because that what they adopted , overall boys were disadvantaged and the equality band widened.
Your assumption here is that boys were disadvantaged by this. They were not. Differentiation does not equal discrimination – not when it involves everybody being given what they need. If I went into a school and gave every boy a $100 voucher to buy videogames and every girl a $100 voucher to buy music (or vice versa) would people be claiming I’d inherently advantaged or disadvantaged one over the other?