Trolley problem is just a pros and cons list made visceral. If the pros don't outweigh the cons there's no point. Before we even bring morality and mortality into this the amount of pros are different for different people to make a decision (even as non visceral as changing a job).
By using much smaller numbers, you are giving a false impression of vaccines. Instead of 1 vs 10k, saying 1 vs 100 is similar to me asking if someone would switch jobs if salary is 100$/year difference when it might actually be 10k$/year.
I'm not arguing against your premise of Trolley Problem but against the numbers. As humans, we can still fathom the difference between 10, 100 and 1000. These aren't big numbers which get washed out into nothingness of 'big'.