I'm kind of surprised that a Prius would be that much cheaper than a similar CR-V-- they used to hold their value extremely well. Maybe between the economy, the recall hysteria and the (relatively) lower gas prices the bottom has dropped out of the used market for these.
The bottom line with a Prius, new or used, is that they've proven to be extremely reliable for a piece of new technology, but because they are more complex, there's more to go wrong. To put it another way, with a normal car there's pretty much two expensive components that can fail-- the engine or the transmission. On a Prius, you've got those, but you've also got a battery, a generator, and inverter and an electric motor, any of which will also be very expensive potentially car-totaling repairs. While the track record of the Prius and hybrids in general has shown that none of these components are very likely to go out, there is still more risk of a major expensive repair than with a conventional car.
It should also be noted that you only really get the benefit of the hybrid system if you do a lot of stop and go driving-- if you do mostly highway driving you'll be disappointed with the mileage you actually get.