It won't happen. While there's nothing illegal if both parties own both games, invariably it ends up on an honor system. Bethesda's content is being transferred either way. Bethesda, understandably, isn't too thrilled with using an honor system, nor with their content getting sent around. Someone could use this as a way to pirate FO3 if they don't already own it.
I do see one loophole, though. It's released as an installer that has no Bethesda content in it. The user would run it, point it to the two directories, and the installer would copy the user's own files around, as well as install a plugin that enables/disables the conversion. This would solve all possible legal issues with releasing it. The mod creators won't be upping any Bethesda content, and the mod users will have to have both games in order for it to work.
Doesn't Bethesda own any scripts and data made with the GECK?
That makes all mods other than texture and mesh replacers put under the company auspices I would think, (with the possible exception of hex-edited files?).
In general I think its a bad idea (if only because its flagrantly against their stated will for their own games). :shrug: