I don't think you can compare a Civic to a Sonata. Different vehicle class.
It's not as ununsual to cross-shop these two cars as you might think. For many people who wish they could afford an Accord but are stuck in a Civic snack-bracket, the Sonata represents all the comfort, quiet and space of an Accord at the Civic price.
I know my wife and I have considered replacing her Civic with a bare-bones, base model Sonata 5-spd, which, given the finance / lease rates, would actually end up being cheaper than a mid-level Civic.
I know JWW on the forum here, my own father with his '06 Sonata and so many survey respondants to Consumer Reports that have been thrilled with how well-built and reliable their Sonatas are.
Smooth, quiet, solid and wonderful to drive on the highway with a massive trunk and tons of interior space -- the Sonata is a great machine. The Civic will be more frugal in fuel and more nimble in its handling... but aside from that, I can't see a reason to choose the Honda.