I just played like normal.
It didn't blow up as being creepy until around the time stuff like Ben drowned became popular, tbh. None of my friends thought it was creepy, either. None of us thought Blue's Raticate died either, just that he replaced it for something better. Blue makes a snarky comment about making your Pokemon faint and then admits to filling out his Pokedex after you beat him. All these theories are fan fiction that became popular and weren't thought of by players back in the 90s.
You felt your sins weighing on your neck.