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.
1. Get out of the way of private actors trying to do things to help. Completely deregulate the manufacture of Respirators, ventilators and other PPE. Get the FDA out of the way of trying new medications and vaccines, etc.
2. Restricting people's freedom to move and peaceably assemble is wrong on it's face so it is irrelevant whether it helps stop the pandemic or not. Would forcibly arresting and isolating in a quarantine camp in Alaska anyone who tests positive stop or slow COVID-19 from spreading? Maybe, but I think that we would still not accept such a course of action on moral grounds.
Again, not positions I hold but that would be my guess on how a die hard libertarian would think about it.