Neem is good for insect control. Many critters don't like it so they move on to greener pasture.
Regarding insects in soil media. Its all part of the whole. Anyone that has a vermi-compost bin will know there are bugs on, in and around the compost. They there and plants arent so thats a good thing. They don't as a general rule eat plants they eat other stuff.
With Vermi-composting we let the compost sit over winter. All the bugs die back (leaving frass behind) then in the spring the compost is ready to get to work growing plants.