You can take the bio balls out, but should replace their filtration capacity with something. a drastic reductiojn in filtration capacity is not good so definatly put sdomething else in their place. I am personally a fan of bio balls in my 55 gal reef tank as they have worked just fine for me over the years, requiring a small amount of regular maintenance. Some people place LR rubble in the sump where the bioballs were as it can provide a fair amount of surface area for bacterial action, as did the bioballs.
I would also suggest more LR in your tank.