The problem is the differential is integral to the transaxle. If the differential needs to be replaced the transmission needs to come apart to replace it. While it is apart that is the time to replace the transmission components. Most shops wont do one without the other because then it is a liability issue if the transmission starts acting up right after they had it apart to fix the differential. Here is the part price and labor time so you can compare it to your shops estimate. This is for a remanufactured transmission not having the shop rebuild it.
I forgot to tell you this is a 5 speed manual transmission.
In that case then you should be able to replace the differential parts and the bearings in the transmission. Here is the info for a manual transmission.