When God commanded killing witches but didn't define the term, did he know it would result in so many deaths?

By definition an omniscient entity such as "God" was and is aware of the nature and consequences of everything that occurs, so the only question one can logically pose is "why"? Since, as you have indirectly pointed out, there can be no reasonable answer, theists are left to throw up their arms and declare their deity's means and motivations are simply beyond human comprehension, and hence, incontrovertible. It's the same pathetic paradoxical (and indefensible) argument which has nonetheless served their purposes so well in all the centuries since its inception precisely because it appeals directly to ignorance and superstition. See "Russell's Teapot."