Well done you for standing your ground! Great you've got the referral, that's often the biggest battle. When you do get to see the consultant, they should also refer you to a nutritionist.
But - to cut the nutritionist's advice right down to the bare essentials - so long as they are getting enough calories from whatever source, and also having another source of calcium at least 3x a day, then no problem (for us, that is unsweetened soya milk 2x a day and 1x soya yog or pudding - all fortified with calcium).
As you are still BF, then you don't need to worry at all at the moment, its all he needs. For mixing with cereal etc, if its not a major part of his diet (ie not the milk he drinks), then you can use any of the alternative 'milks'. Not goats/sheeps milk, as they have very similar proteins so you should treat as if they are cows milk. But oat or soya milk - make sure you get the calcium fortified one.
However - re soya - quite a high proportion of those allergic to CMP are also allergic to soya (I think around 50%). So either introduce carefully, or avoid for now. We never had a problem with it, thank goodness, but it would be a right PITA to have soya as well as dairy ruled out.
If, in the future, you want to stop BF before the age of 2, then you need a specialist hypoallergenic formula eg nutramigen or neocate. They taste vile, but the babies do get used to them if you introduce them gradually. Your consultant can prescribe them. After the age of 2 its fine to use soya or oat milk (fortified).
And well done again for standing up to your ignorant GP. I wish experiences like this were isolated, but unfortunately they are not. I remember taking DD1 into the GP as I thought she had developed asthma, to be told 'we don't like to diagnose them this young, lets wait and see'. A week later she was hospitalised with a serious asthma attack. And I have many more stories like that. Parents know their kids best and the doctors should blooming well listen.
Rant over
You got the result in the end.