The main thing here is to respect the writer. The writers don’t have to do everything we want them to—we make suggestions. The ideal would be to give an editor a proof and have all your suggestions meet with approval. Sometimes you notice that your suggestions have not been taken, so if something bothers you, you try again. Sometimes you wear them down, sometimes you cave.
This whole interview is worth a read, particularly the part where she talks about the New Yorker’s foolproof system for editing. (Hint: it has more redundancies and safety nets than, say, Congress).