how to remove 2 bolts locking harness on 1998 Honda Civic LX AT ignition switch?

Small ball peen hammer and a 'sharp' pointed punch. All you need to do is turn each bolt a little bit, then they are easily removed. Another method is with a hammer and small chisel, cut a slot or groove in the head of the bolt to allow a flatblade screwdriver to be used. Shop method, left hand twist cobalt drill bit set and a reversible drill, you may not have all of these items.

either drilled out or grind off.