Yeah because she'd totally be kissing a rat and not just nuzzling it the way thousands of pet owners do with their animals. I think you've been looking at too much sick animu.
Yeah. I don't see it in any sort of romantic or sexual context. That would just be creepy. I see it more the same way I do when a can reaches up to her caretaker's face the same way, which makes it adorable.
Samus seems to have a bit of a maternal side to her (Note: Haven't played Other M yet), so I wholeheartedly approve of this, and her saving of Pikachu in Brawl.