I find myself in agreement with both sides here, but mostly with calypso.
Like many Brits, I find it very hard to leave out the "please". However, I work for a non-British carrier whose philosophy is very non-British (surprie, surprise!
) and who cannot understand why their British employees feel the need to include it.
The manner in which things are said can, as calypso points out, make a huge difference, and if the SOPs state that you leave it out then it is a little unprofessional not to make an effort to leave it out.
After all, saying word like "please" and "thank you" do not comprise the entirety of the atmosphere on the flight deck.