I think you should congratulate him, but you should tell him that he shouldn't want to be getting sober for anyone but himself. Its true and it will also prevent him from thinking you're leading him on - because obviously congratulating him isn't leading him on but some boys are fucking weird and take everything as a reason to think you like them.
Congratulating him on being sober isn't leading him on, and it's a big thing he's done that deserves acknowledgement. But if you're really worried about him misinterpreting how you feel about him you could always include a not so subtle hint about how glad you are to have been able to help a friend.
Yay!