I have experience with both and I certainly don't find anything comforting in church bell ringing, and frankly I'm sure people in Turkey (atheists included) are used to muezzins and generally not annoyed by it, just as I am to church bells and live with it because I have no choice. That said, I believe that the way you describe it is how you perceive it, but from my experience I wouldn't call it whiny/whingy. It's short, in Arabic, and basically a singing version of call to prayer. Just as church bells have some form of tune to them, so does the muezzin's call to prayer. If we are to name what one might find personally comforting, I wouldn't mind daily gospel music played for the neighborhood by the local church, but I'm sure someone will find that discomforting as well. And to be clear, I am not a Christian.

My main objection is that if you have religious freedom, then either all churches/mosques/temples get the same freedom to call to prayer or none does. The exclusivity of church bells in Europe and muezzins east of Europe is the basic conflict of fairness here. So, realistically, given that we cannot allow them all, including pagans, satanists (death metal?), the most logical conclusion would be to generally disallow, with exceptions where the population insists on it.