What I don't agree with is saying that there is merit to their not taking advice based on it may debunked later.
I think this is more of an issue in adult medicine. Vaccines in children are pretty straightforward. I do see kids whose parents refuse vaccines. I figure it is better for the kids to be seen and have me tell their parents I think they should get their kids vaccinated than not to be seen at all. And often they do end up agreeing to some vaccines.
In adults I've seen goals for BP, lipids and A1C's change many times over the years. How often to get PSA's (if at all) is still being argued. The guidelines for mammograms, colonoscopies, etc in the elderly also have changed and are still being debated. Often I will tell a patient I am giving them my best advice but if they go down the street and see another doctor they may well tell them something different.
I also see a lot of polypharmacy and have a good deal of sympathy when a patient says "Dr X wants me to take this but I don't want another pill". In that case I explain the reasoning and let the patient make the decision. Sometimes the benefits of medications given to meet "the guidelines" are marginal and the implications of giving them along with ten other meds are unknown. Basically it's my job to give the patient my best advice and their job to decide what to do with it.