The FACTS here are really very simple:
1.) We have seen drastic reductions in the occurrence of just about every disease for which vaccination has been widespread for a significant amount of time. Some like Polio have been practically eradicated where the vaccine is prevalent and Smallpox has been completely eradicated.
2.) When people stop vaccinating against a sickness those sicknesses make a resurgence. This is currently happening with Measles in areas where larger groups of people do not vaccinate.
3.) Every major health organization, medical association, and medical journal, EVERY SINGLE one without exception endorses vaccines. To posit that all these people are part of a huge conspiracy is frankly ridiculous.
4.) Whatever your beliefs in Hashem are, the one thing you can’t dispute is that the natural world without modern medicine is a brutal and terrible place; and yes, he does create physically imperfect babies and allows for people to improve on his creations through medical science. Visit the Children’s ward in any hospital or look at the rates of child mortality in countries where vaccination and modern medicine are not prevalent. Again, the natural world without modern medicine is a brutal and terrible place to live in.
As far as risks yes there are risks, in the same way that there are risks to wearing a seat-belt in a car, or having electricity in your home. There are risks to taking any kind of proactive approach to anything at all. If you DO something-anything you create some risk. However not doing anything will cause a lot more harm.
These are facts.