You could certainly go for a second opinion(and as others have said, make sure the therapist is a gender specialist!), but perhaps it may be better to address the doctor's concerns directly and work on making your son feel more sure and comfortable about where he is going. Spending time on forums such as these or presenting as female online in general may help, allowing him to get more used to feminine pronouns to see if they feel right. Even better though, encourage him to spend time in a female role in person, even if just with you. Makeup and clothing are cliches, but any physical presentation can go a long way in helping sort things out.
I know that presenting as female in therapy was a game changer for me, and helped show my therapist that I was serious about my feelings. While requiring "real life experience" varies country to country, if it is practical and not harmful to the individual, those sorts of experience do help therapists and doctors in feeling more comfortable that the person is on the right path.
Making other progress in the meanwhile may also help not only in alleviating depression but showing the doctors what they need to see as well.
Having said that, you could ask for some androgen blockers as a hold over. They are commonly prescribed for hair loss (Propecia, generic name finasteride, is an anti-androgen) and other things for men, so shouldn't be controversial for the doctor, and they may help delay any further masculine development since he is still young without causing any irreversible side effects in smaller doses.