Counter-counterarguments.

That assumes the 999 are in a position to stop the 1. Assuming FTL travel/communication/detection is never possible, reaction ability is always going to be limited. A relativistic projectile aimed at a planet can be a silent civilization killer.

This is more about cautiously reacting to the possibility of hostility in the very high stakes scenario of first contact, not the confirmation of hostility. In the room analogy, we don't know who has the gun, whether it's truly 1 person or 0 or 100 or 500, if most or all of the 999 are blindfolded or willing to defend newcomers, whether overpowering the violent one(s) is actually possible due to everyone being spread out and any guns having functionally unlimited ammo, whether other people have already been taken out for just showing up or resisting, and whether all of the above even matters if the aggressor gets a kill shot off before any of the above takes effect.

Evolution is inherently a competition for limited resources with winners and losers, so violence innately comes with the territory. Even grass and trees are in a war for sunlight. The concept of peaceful cooperation may be common due to the individual specialization likely needed for a species to become space-fairing, but it'll be a higher level, more abstract idea, and the universality of other species applying it more broadly cannot be assumed.