If a bedtime routine works, and doesn't have consequences (like rotten teeth or needing to get up in the night for a wee) then stick with it. I've always given my kids a cup of milk after they've got into bed, I can't see a problem with it and I've never heard of milk causing dental problems.
Are you sure your dentist understood it was milk you were giving him and not juice? Usually the best thing to do with professional advice is listen to it, and pick out the bits that suit you and your child. If giving him milk when he's got into bed is what feels naturally right for you to do, then do it.
I'd go back to it, some battles aren't worth it but if you do feel you need to stick this one out, it'll just be a case of time and him running out of steam.
The Dentist has advised against having milk last thing at night because there are sugars naturally in milk, which can cause decay. We always gave milk last thing at night but have had to make a few changes, like you. Could you try a beaker of milk downstairs, make it more grown up for him. Then use the lided cup with water in? Not sure it will help, but stick with it, its the right thing to do for his little teeth!