If it is ready to bottle, you can go that route. A couple days sitting shouldn't do that much damage unless you're keeping it really warm. If it's under airlock now, it's not like new air is getting in.
Personally I'd say that unless you're planning on having it sit in that container for several more months, any manipulation you do now to reduce headspace (either adding marbles or racking it again) is going to cause just as much or more oxidation as leaving it where it is. I don't have any data to back this up, but that's my guess.
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