I think you are confusing people being civil and not bigoted or misogynistic (or whatever) with what most people think of as "stupid political correctness" which is when it's gone overboard and used to try and silence people or just ruin someone else's time.
I don't think I am confusing the two, Simon. It is all part of the same package.
You give the example of "...it's also politically incorrect to say happy christmas to people when it's intended with no malice or insult." This example just highlights the ignorance of those who believe that their intentions are exemplary and because of that, that their actions are justifiable regardless of how those actions effect anyone else. It reminds me of someone who drives a transport truck through my garden because it is the shortest route for them and then says "...oh, but I didn't mean to kill your garden! I was trying to miss the potatoes and I didn't hit the peas! Be grateful for small mercies..."
So what if no malice is intended? It is the consequences to others that are important. Political correctness isn't about you...it is about the ones who are marginalized/silenced by dominant culture.