That is a subject I've often wondered about, but hardly ever see it mentioned. Yes a puller with a pointed center bolt can expand the crankshaft if hit hard enough. That is just one of the reasons I keep preaching not to belt it with a sledge. An ideal puller (like the OMC) has a flat end on the center bolt, with only a small point to keep it centered on the crank. The flat contacts the crank end before the point goes deep enough to do damage.
What to do now is up to debate and opinions. The threads are hard and difficult to fix. And of course if the nut is hard to turn on, it defeats the benefit of using a torque wrench to tighten it properly.