I don't think most libertarians would interpret doing something that has such an indirect pathway to harming someone as aggression. If you're an at-risk group and somebody comes too close/coughs on you, I could see that being perceived as violating the non-aggression principle, but not e.g. two people having drinks at a bar together, which increases the chance of a virus spreading, which increases the chance of you eventually getting it. Especially when trying to stop that indirect violation would be a very direct violation of the rights of the bar owner and patrons to property and free association.
However, if we want a society that's not helpless against deadly pandemics, I don't think that means we have to abandon libertarian principles. We just have to apply them in a slightly different way.
That said, the libertarian inside me worries a lot about how the surveillance mechanisms we setup to deal with the current pandemic will persist and be repurposed for more nefarious means after the current crisis is over.