Sounds like a good prescription for ruining the cranks - once they start to loosen you'll still be applying some torque that will tend to deform the square hole and may make it impossible to properly tighten them later. Get the proper crank puller tool for your crankset. Not too expensive and you'll need it if you plan to continue maintaining the bottom bracket.

Flipping the spindle over is likely to make your chainline even worse but in the opposite direction. Sounds like you need a shorter spindle - they come in various lengths to accommodate doubles, triples, and variations in frame geometry.