Google "Justin Bailey", and then get back to me.
No, it doesn't ruin her appearance in that game. Does it detract from Samus as a character? I suppose. Enough for me to worry or care about? No.Mind you, just because it didn't ruin the Metroid franchise doesn't mean it doesn't ruin her appearance in that game. It's out of character and is inconsistent and ultimately detracts from Samus as a character.
When I think of Samus, I don't think of the sexualization. I don't play Metroid with the Justin Bailey password. To me, it's not a part of her characterization, it's just an Easter Egg in the game that I can ignore.