It's not pollen since your plant is holding on to seeds, which means it's female.
Very few junipers are monoecious.
If you spray it down with some soapy water, most spores will wash away with it. Soapy water breaks the surface tension the spores use to stay dry and mobile. It will not get all of them, but a good couple trillion will be knocked down to the soil. Two or three drops of dishwashing soap like Dawn should be enough, and don't hurt your plant.
By the way, about 99.9999999% of all spores (bacterial and fungal) are harmless to humans. So don't bother wearing masks when working with this stuff. It's pretty amazing how much things in nature don't even care about us. The list of microbes that do and the ones that are also naturally present at any given region, can be fitted on less than one whole sheet of paper.
I'm not saying you should rub compost on open wounds, but I do think it's remarkable that so few things are out there trying to eat us.