Given the relatively small difference in the prices you mentioned I would pick the Prius. For me, it would be a no-contest. Some may argue that the manual transmission Gen 1 Civic can match the fuel economy of the Prius but the fact remains that:
-You may have to work at it on the HCH.
-The 2007 Prius is a potentially safer vehicle with a full complement or side and curtain airbags- please correct me if I am wrong on this one.
-The Prius is less polluting than the MT HCH.
-The Prius offers more versatility in terms of cargo space.
-The 2005 HCH is a 2 year old(er) model.
-History ! Hard to know the full history of a used vehicle. Many of us find it conforting to pay a few grand more and start with a clean slate.

Cheers;

MSantos