Don't know if they gave you a quote or not, but standard transmissions usually aren't that expensive to deal with; certainly nothing like automatics. I know I had to replace them on both a Toyota and a Mazda and in both cases they ran about the same as a clutch job. Another consideration, depending on how you feel about the car, is putting a used on one on there. If you're not looking at keeping the car for the long haul, then it's a perfectly viable thing to do.
You never mentioned what kind of car it is, but you might check eBay and see what a used tranny is running for your car.