Brad,
You are correct that Lightbox is gone in the Kentico 9 (I checked a fresh install I've done and its missing), but in an upgraded version (from 8.2) the gallery is still present, so it will not remove it if you upgrade (though I have not tested to know if there is any issues running it).
As far as your other issue, I would be really surprised if a .NET framework upgrade would fix a browser compatibility issue, but it may. I would also suspect that the Lightbox javascript is probably not totally compatible with IE 11, so you might want to explore that as a potential upgrade point as well.