There is no proof, that I am aware of, that being polite on the flight deck, saying please and thank you etc. has ever impinged on flight safety and any suggestion that being polite is unprofessional is purely in the minds of those who elect not to do so.
The fact that a company actually puts guidance/instructions in it's SOPs to the effect that such words and phrases are improper often only reflects the opinion of the individual with responsibility for writing that particular section or chapter and can be amended out with little difficulty - no worthwhile aviation authority is going to get worked up over such trivia.
My most unpleaseant time as an FO was when flying with an ex USN pilot who was never heard to be polite to anyone. The atmosphere on the flight deck was always tense and generated a fertile environment for errors, large or small.
In thirty six years flying I have tried to maintain a correct and polite stance when dealing with all issues, normal or abnormal and have never been censured for it once.
I believe Atropos and dogcharlietree are correct in their approach to this issue.