This presumes that anyone on the Internet owes a troll their time and effort to discern between a fool, an extremist, a shitposter, a troll or a misguided but earnest individual who shares a genuinely held but scientifically false opinion.
There is more at stake in public debates than just the back and forth between troll/skeptic/questioner and someone responding to them.
If you benefit from such a good idea as vaccines and the rather obscenely massive benefit they have delivered to humanity, you have a moral obligation to step up and - even if rarely - throw down in a debate in their favor, when presented with such a tremendous opportunity. It requires the tiniest of efforts compared to the scientists that manage to give us these vaccines across decades of their efforts. Which also doesn't mean a person can't be lazy and free-ride on everyone else that is putting in some group effort to intellectually defend vaccines, of course. There are always free-riders.
The public skeptics and trolls are doing everyone a favor. They're being public about it. They're providing an intellectual and social opportunity that should be taken advantage of, eagerly. It's wonderful that they exist. They provide an opportunity to educate/inform, not specifically the troll or skeptic, rather, everyone else that is reading along. There is no avoiding the consequences of public debate on such important ideas, there is only to engage or give ground to the other side.
There is no way to differentiate a troll from either a fool, an extremist, or simply one who happens to not share the opinion of the reader.