Both of them have 1300cc engine. But upto my experience a brand new 1.3 Gli is far better than a honda hybrid. A hybrid civic may give you upto approx. 750 kms in city while a Gli will give you approx. 550 kms (calculations based on my experience) on a full tank. Parts of civic are expensive as compared to Toyota. And above all a new car will have less problems as compared to the used ones.
If you want to go for a hybrid, go for Prius but with a low milage and a proper auction sheet (as milage is mentioned clearly on auction sheet.)