What I'd do, at the risk of seeming childish (from what you said about her, she seems the sort that would find that charming) would be to get the plush toy and fix the flower in its hand somehow (rubber band, twist tie, or string).

I don't think you'd come off as desperate, but that also depends on how you present it. Since it is something you know she likes, I think the only thing you risk coming off as is thoughtful.

Boost's "I missed you more than I thought I would" for her return is a great line. I'd use it.

"plus all the girls I worked with said the plush would be a good idea"

I have never found taking advice from other girls to be an entirely bad idea. Especially if they are friends of hers or know her personally. They know sides of her you have never seen, and can offer excellent insight or suggestions. You just don't want them, or her, to get the impression you are incapible of coming up with ideas on your own. Personally, I'd think of them a bit like "training wheels", serving a purpose until I got to know her better.