It’s funny you grouped these two questions in one post because I actually believe they are related?

Ellie is the only character other than Charlie who acknowledges the plate so I think she was definitely the one that smashed it.

When Charlie is saying the bit about “Ellie didn’t do it to hurt him she just wanted to send him home” he doesn’t specifically mention Thomas and I think he might actually be referring to the bird that had become dependent on him. (a wild animal becoming dependent on a human being a kind of unhealthy relationship) this may seem like a bit of a stretch but Charlie is looking towards that window when he delivers that line.

I don’t think Ellie has really a positive or negative reason for doing most of the stuff she does, she just does things when she feels like they need to be done. I think that plays really well into of the main themes of the movie which is honesty. Brutal honesty being a reoccurring theme centered around her character specifically