I think the answer to the above question is "yes". I vaccinated my kids, but I'm not sure it's right to force vaccinations. However, I would hate to be the parent who had to explain to my child why their life has been forever altered by a disease that could have been prevented with vaccination.

Cui bono.
In the case of polio, (or another disease that kills many), when a vaccine is developed and proven to prevent polio in 90% of potential patients and is proven to have few side effects wouldn't almost all voluntarily take it? Is it not enough to provide all the facts and allow people free will with their health? What percentage of people will take the risk of a deadly disease (polio) in order to avoid a lesser long term risk (e.g., mercury.) Government has no constitutional power to force vaccination, but assisting in educating people on the risks could promote the general welfare while allowing individual free will.

Could this be another case of effects on business interests and power seeking bureaucrats taking priority over individual rights? Is it so important for (arguably) fewer employees to take time away from their jobs due to flu that the entire population be subjected to (arguably) damaging mercury? Or is it more likely that bureaucrats don't like their "wisdom" being challenged by mere citizens, and pharmaceutical companies encourage such acts because wide use of vaccines is good for their bottom line?

Shouldn't the action of government (not that any such action is constitutional) be better directed at encouraging an alternative delivery system that doesn't include mercury?

I don't know. I was a young boy before Polio vaccine. I had four younger brothers and we all experienced measles, mumps, and chicken pox as did every other child that we knew. I can't remember anyone that died. But we were all free range children with immune systems fortified by the world around us.
Polio vaccine, I think probably a good thing, but it's been coming back in a mutated form for 15 or 20 years now as has nearly every other bacteria and virus that we treat with both anti-viral and anti-bacterials.
And we're now letting thousands of S. and C. American children into the country not only not vaccinated for our standards, but also bringing in viruses and other infections that we're not vaccinated for. I'm just not convinced that we can eliminate all potential dangers to human life and many of what we're trying to eliminate are really more nuisances to humanity in general, though serious for some individuals.
I'm just not sure we're making progress, or the right kind of progress.

I am confused by the parenthesis. so it is hard to respond....if we look at legal certifications for firearms vs those who do not vaccinate....there isn't much info. I know this. viruses and diseases mutate quickly. faster than we catch up. don't vaccinate. fuck us all over because of mutations...let's tidy those up...

Do you have a right to endanger other people? If you choose not to be vaccinated, can (should) you be quarantined? It is like drunk driving or owning a handgun without safety certification. ("I don't need no stinking certification!") You are perfectly free to live on your own in the woods. Do without vaccination. Go naked in warm weather. If you want to live in the city (suburbia, village), then you accept the social contract. In _The Fountainhead_ Howard Roark differentiates wearing clothes on the street from letting other people tell him how to design houses.

(Lest we have a different discussion, entirely, vaccination has good science and good medicine behind it. It is not the same thing as having 666 tattooed in bar code on your forehead.)

Vacination is a great public health policy. Our society is too statist, and that affects the implementation of even good policies.