Pilots are supposed to be fairly mature adults and therefore this shouldn't really present much of a problem.
If the ops manual prohibits smoking in the flight deck, then anybody (Captain or not) is on very thin ice if they choose to ignore this stipulation.
The fact that somebody smokes, does not mean that they have either the right or necessarily the inclination to smoke in places where they are prohibited from doing so. If you find somebody in violation of this ruling then assuming you could not sensibly resolve the matter, refuse to accept this crewing pairing on the grounds that it would be in violation of your companys rules.
If you are concerned that this would have a negative impact on your career or interpersonal relationship with an individual then you need to consider two things. Firstly what other violations of regulations would you be equally supine about ? Secondly why raise the issue if you are not individually prepared to address it ?
The Captain is an adult, you are an adult, deal with it. If you are too timid or concerned then either put up with it or move on. Sorry but although it might be an uncomfortable issue to confront, if you intend having your own command you will have to deal with thornier issues than this one.