you really have to decide what you want, and test drive both.
i love my si sedan. and it easily gets 33+mpg on the highway. even in the winter, its 30+. the engine is not for everyone. i haven't had any 3rd gear issues or rattles or visor problems with mine, knock on wood.
sometimes my parents complain about the amount of noise on the highway, which is substantial since you're doing 3500rpm at 70mph, and there isn't much in the way of noise isolation.
my parents have "borrowed" my car for the past 5 weeks...i miss it so much.
in short, the Si really is a love it or hate it car. really interested to see what they do for the 2012 Si.
also, if you decide to go for the civic, see if there are any 2010s still on lots, i doubt much has changed and you may be able to find a deal. i got my 2007 sedan with navi & summer tires for 22k OTD towards the end of 07