Are you seriously suggesting that President Juncker is just another faceless civil servant. If we had a civil servant that behaved like Juncker, the PM could sack them. Again, how can anyone in the U.K. get rid of Juncker.....
Of course, he is more powerful than Jeremy Heywood, but then he's also more democratically accountable, as he's selected directly by the European Parliament, having first been proposed by the European Council. So the people you vote for have a direct say in who is appointed, just as they have a direct say in what that appointee does.
I believe each president of the commission serves a five year term, and as he was appointed in November 2014, the processes for replacing him will be underway shortly.