Hone school 99.7% of the kids because of .3%? That seems reasonable.
Most people vaccinate, so I fail to see why they would be so afraid of disease that they would stay home.
Life is full of trade-offs. You know before you take your kid to get vaccinated what the risks are and you know if you don't, you may not be allowed to send them to school. Make your decision based on all of the information at your disposal and live with the consequences. Freedom demands that you live with the consequences of your choices.
You know the consequences of not buying health insurance. Do we call this freedom now?
As to your other argument: You're arguing apples and oranges. The feds have no constitutional authority, with all due respect to SCOTUS, to enforce SCObamaTUS-care. The states do have the authority to require you send your kids to schools...unless that's hiding in the commerce clause or 14th amendment too.
So pretend we're talking about state-level bullying. Like Massachusetts's individual health insurance mandate.
Romneycare equivalent to the thing you're defending.