If you need an automatic, then a Civic HX or a Civic Hybrid is going to be the way to go, but if you want reliability then avoid the automatic! but even a 2005 civic hybrid has a blue book value of $3,700 to $5,100 depending on condition.
Fuel Economy
Is a search for Honda's with automatics, I limited it to 1984-2006 to keep the vehicles in your price range, altho a quick search on KBB.com shows that the 2006 civic hybrid jumps in price and is not in your price range.
It boils down to all of the years of Civic HX with a CVT transmission being pretty close to each other as far as gas mileage goes, and the 2002-2005 civic hybrids also have about the same mpg figures, with a jump when they made a bunch of changes in 2006 and onward.
With a manual transmission you will get better gas mileage and you will pretty much avoid issues with the transmission, because a manual transmission wastes less energy the engine isn't working as hard so everything else is going to last a little longer as well, but some people have their reasons for not driving a car with a manual transmission, but I think most of us agree that you should be well informed about the benefits.