Yes, those refs in @section lines are admittedly a bit of a hack, though it would be nice from the pure orthogonality point of view if they didn't have to be ruled out. But it sounds like supporting them robustly might be quite a hairy mess to implement, of questionable value, and perhaps not worthwhile for such a marginal case even given that the restriction would otherwise have to be documented (if only by pointing to a more general principle about not having links where they don't belong).
In my hack, the links reappear in the section titles that are in the document body, which on the surface seems a bit absurd (go to self??) though in a typical PDF reader's continuous scrolling mode, they have the pleasant side-effect of being a one-click way to bring the section to the top of the window.
I am already working with a patched texinfo.tex, so I would be happy to be a guinea pig (and likely early adopter) for your proposed table-of-contents feature if you want one.
Thanks,
dB