User blog comment:The.Outsider/Sequel/@comment-69.85.234.253-20130125153442/@comment-27202257-20130125174038

In high chaos at least, there clearly were some people who didn't like Emily being on the throne. We see Corvo knocking one such fellow out in the ending.

But yes, as Snowkeeper put it, we know for a fact that in both low chaos and high chaos (when she survives), she goes on to rule for many years--even leading Dunwall into a Golden Age in low chaos. In all likelihood there were people who didn't like the idea of her ruling the Empire--child rulers have historically been seen as easy targets for potential usupers--but clearly Corvo did a pretty good job of keeping her safe through that.