It will not harm your soil biota to use Milky Spore, it will simply be another beneficial living in your soil.
Paenibacillus popilliae (formerly Bacillus popilliae) is a soil-dwelling, Gram-positive, rod-shaped bacterium.
It only causes disease in beetle grubs. It won't even harm the cicada larve living in your soil, should you have some of those.
We love visitors, that's why we live in a secluded cabin deep in the woods. "Buzzard's Roost (Asnikiye Heca) Farm." Promoting permaculture to save our planet. https://permies.com/wiki/redhawk-soil