I do think that the simplest way would be to convert the current (pretend) footnotes to proper footnotes.
Peter Kahrel’s script should work. When he says “endnotes”, he just means text at the end of the chapter, since he wrote the script before InDesign had real endnotes.
I should definitely be possible to get that script to work, provided your (pretend) footnotes are only a single paragraph long and have a unique style applied to them.
By the way, I see at the bottom of that page that he offers (for a fee) to help with the conversion. Not sure if that’s still the case.
I will definitely consider adding something to Footwork to convert it’s footnotes to endnotes, since this is useful not just for ePub export but actually for managing the footnotes. However, it will take a while before I get round to doing so.