Hi, your game sounds really interesing. I love metroidvanias and am making one myself. I think a good way to implement non violent options in games is to reward the player for using that approach. Eg perhaps when an enemy is stunned rather than killed they drop a valuable powerup, but if they are killed they explode and it is instead destroyed. You could also use it for dynamic changes in gameplay, eg if a robot enemy is stunned perhaps an electric field will appear around them, while the robot is incapacitated it can't chase you but now becomes dangerous in a different way as if you walk into it you'll get hurt so depending on what else is going onscreen it becomes a different kind of obstacle. You could set things up like a master switch that pacifies all robots in an area, but to get to it requires a puzzle or a very difficult platforming challenge to get to, so it gives the player a choice to either go in guns blazing, or go off on a difficult tangent for a while to get a more substantial reward. Some quick ideas for non lethal ways to handle enemies:
stealth/invisibility (maybe with a time limit or other limitation, so that there is a constant challenge pattern)
Using shadows to hide in for safety
Freezing enemies (eg the freeze beam in Metroid)
Taking control of enemies (eg like in Oddworld)
Playing dead
Getting them to fight amongst themselves
You could check out some non metroidvania games where the protagonist is in a dangerous world but can't actually defend themselves for ideas on these kind of gameplay elements. Off the top of my head stuff like Limbo/Inside, Oddworld (the first 2 games) - I can't think of any more at the moment but there will be a bunch....