The expectation is higher in the first case, but then chances that it's your particular kid would be 1/group size. So I guess it would be more accurate to have 5 kids in the first group to make it 1% vs .95%. That's still not any better is it?
Do you rather have your kid to have big N% chance of being abused, or small n%. At a micro level, you might get more control, but at the macro level, the results in aggregate are what matter.
It's obvious there's problems with either rate you'd choose for either task.
We have varying degrees of exposure / vulnerability within the populations. Neither one really directly leads to a "risk per unit of exposure of child" or "risk of a given person being an offender".
But it seems like you have some pretty motivated reasoning going on: it sure looks like religious organizations have not done well, and are relatively likely to be much worse per unit of youth exposure.
An important fact that gets overlooked is that religious organizations are one of the few aspects of civil society that put children in contact with adults. Really the only secular organizations that do so at a large scale are daycares, schools, and sports. It makes no sense to assert, as OP did, that churches are especially full of pedophiles, without offering a comparison against the other environments where children are exposed to adults.
Religious organizations have a) smaller number of personnel, b) fewer youth contacts in total, c) lower hours of contact per average youth than your comparison organizations. We can debate about the importance of each of these in the denominator, but they're all signifiers.
Worse, you're trying to compare numbers for schools that include student-on-student sexual violence (the vast majority of cases) to complaints against staff and clergy for churches.