You can talk to your doctor in confidence about alcohol use.
But as a military doctor, if they feel you are a risk to others or yourself then they will downgrade what work you can do. That's only right, as it protects you and your colleagues.
How they judge how much of a risk you are depends on how much you are (ab)using alcohol. They can only gauge this from what you tell them. You haven't said here what your drinking habits/quantities are so I can't offer any suggestion on what they'd say about it.
If you feel brave enough, tell this thread how much you drink and how often. It will help others here to determine what's proportionate when they advise you. If you don't want to do this, that's fine.
Lastly, you have options outside of your medical centre. There are alcohol charities you could contact anonymously, explain your situation to and get advice from without having to involve the MoD. They may be better placed to give you the answers you seek than this forum.