When you get the plague crisis settlements infected by the plague take damage but this damage applies to every unit including traders which aren't controllable. Trade routes getting knocked out because they travel through a settlement that has plague might be thematic but because you have no control over them it feels really bad to lose the units.
I know trade routes are not guaranteed as they can be plundered but you can always escort traders if you're concerned about raiders. You can't do anything about the plague though.
Also please give us a trade menu so we know what trade routes are available. This could help if we're keeping the plague killing traders as at least then we will know which trade route is no longer happening.