Pathogens don't "learn". They evolve, ok. They adapt, ok. But they aren't sentient. They are not thinking. And especially they aren't thinking "hey, if they vaccinate, they won't die anyway, at least not as fast, so let's get more deadly!" This isn't the fucking Pandemic flash game for crying out loud!
There is no interest of killing a host for a parasite. It's an side effect. Unintended, and actually harmful for the parasite in the long run. Just like poisoning the seas is harmful for us. We ain't some comic book villain who does it for ... well, for being evil. We do it 'cause it cuts costs. The oil spill is only the side effect, not the reason we do it.
So yes, they COULD get more deadly because we don't die as fast and a more deadly mutated strain would kill itself off with the host if there was no vaccination. But that is hardly an argument against vaccination. It only means that at worst we're with vaccination where we are now without. AT WORST. If, and only if, the pathogens mutate in such a way that they get more deadly. Which is neither in their interest nor anything they would (evolutionary) strive for.
What's the benefit for a pathogen to be more deadly? Killing the host is actually bad for it, since that ends spreading (with this host at least).