That all depends on the severity of the illness you would get if you got sick, no? Otherwise your math is missing a vital piece. Otherwise you are missing half of the equation. You are trying to draw a conclusion by only considering half of what you need to consider.

So let's imagine that you have a vaccine against the common cold. And 1/10,000 times (I made it 10 times less likely than your number) it is given it causes encephalitis and some degree of permanent brain damage. And, if left untreated, 1/10,000 times those who catch the common cold get pneumonia, and 1/100 of those people die.

And let's say that the cold vaccine reduces your chance of contracting the cold by 1/2 (about standard data for things like the flu shot.) So that means that without the shot you run a 1/ 1 million chance of dying from pneumonia, and getting the shot reduces that to 1/ 2 million.

So.

You can get the shot, and run a 1/10,000 risk of encephalitis and brain damage in exchange for dropping your 1/ 1 million chance of pneumonia to 1/ 2 million.

Or, you can not get the shot and just stick with that 1/ 1 million chance of pneumonia.

That's how you figure it properly.

Your description was, unfortunately, how most non-medical vaccine advocates see it, they presume 100% effectiveness that isn't there, and presume no side effects, which also isn't there, and presume death if the vaccine isn't given, which also isn't accurate. Given that panoply of inaccurate information, not surprising that they are so adamantly pro vaccine and treat anyone who questions it as daft, no?