First of all, I want to say that it's a pretty cool plugin that you created here. I love plugins that work out of the box and have no settings panel.
In this case, I think adding a small field under Settings > Media for Maximum Comments Embed size would be very helpful.
The main reason is because most sites use oEmbeds to embed items in the post thus making it full post width. Comments content area usually have less width to begin with. Then you add threading on top of it. This breaks the layout.
Hope you will consider that request. Thanks :)