I think the point of miracles is not to take away decisions but rather to take away consequences. In the scenario you present, the killers of the resurrected men still made the decision to kill, but the consequences to the dead man were changed. Free will still happened in that scenario; the consequences changed. Decision-making, whether from free will or “dependent origination” (as the Buddhists suggest), is influenced by all kinds of factors. If a God or “Engineers” tweaked the simulation to bring in unexpected variables, that doesn’t change the ability to react to those variables, does it? If a tsunami born of an earthquake is bearing down on you, you will likely choose to seek cover. Does that decision change if it’s an advanced alien landing in a giant star ship with lasers blazing or a God parting the Red Sea? Your decision to stand your ground or run for cover is still your decision.
The question of WHY we might be in a simulation is the more interesting one: Is it possible that the “Engineers” in base reality are using this simulation process to sort out who are best candidates to join them in base reality? That this simulation is a training ground and a testing ground for those candidates? In every grand myth we tell, there are dark forces (including “gods” and “fallen angels”) that decide to ruin it for everyone else by behaving badly. Assuming a civilization is advanced enough to run simulations indistinguishable from reality, keeping the peace and making sure that active and free citizens in base reality have truly “grown up” and choose to be cooperative and peaceful participants in “base reality” society might be the price of the privilege of living there. Whether this is an advanced alien species (which any “god” would likely be idenified as) or even our civilization 500 years from now, the reasoning behind this simulation and its use of miracles and “grace” to help those who seem like ready candidates to move on to base reality would be not only reasonable but an essential part of the process.