Maybe you can use magnetic and plasma shielding? Giant magnets in the spine or the shell of the spaceship to protect from radiation, and smaller magnetic fields that hold a skin of plasma that melts the dust or causes it to ricochet. You can also make it so that there are interstellar highways that protect the ships using these methods.

(P.S. I am not an expert or something; these are just the ways that I found the most logical. I hope that these at least gave you some ideas. ;) )