I would go to an orthopedic vet for a consult! Go to
www.acvs.org and do a search for one in your area.
Just tell your vet that you want to get a second opinion. He should not have a problem with that.
A specialist usually charges $100 - $150 for a consult.
Honestly, that muscle atrophy is very common! He will get muscle back when he starts to use that leg. Since it has been a couple of months, just to be sure everything is ok, do get that second opinion. Also, if you cannot afford physical therapy, then ask if you could have a home based program. A good physical therapist will write one up for you and that will probably not cost any more than $150 (I think).
I would never amputate a good limb...EVER. What people fail to understand is that if you do that and the dog ends up with a problem with another limb that really cannot be repaired....he is basically up a creek without a paddle.