It seems to me that this sort of thing would not be easy to implement, because you would have to incorporate Facebook code into the theme’s code, which is problematic on a number of levels.
You shouldn’t be modifying the theme’s core files anyway, since, as you’ve realized, you lose all your changes with every update. What you should do instead is to disable WordPress comments and insert whatever code you are using into an action hook widget area. You can then update the theme without losing your changes, and if (when) Facebook changes its code, you can make changes from the widgets pane (easy), rather that digging into the theme’s files (pain in the neck).
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