First I what I typed before, I should clarify. Officers who had 40s can still carry them, but the most recent recruit class had to choose between the 45 and 9, and that is the way it will be until it changes......(when I got hired, we couldn't carry the 45 because they were worried about the cost of that ammo) An officer that already had a 40, can not replace it with a new 40.
I can't give you the exact reasons why, as I wasn't on the committee that made that recommendation that was approved. With a governmental agency, cost (of ammo) is always an issue, and it seems our department always wants to get down to only having to buy 2 types of ammo. The cost of the weapons is not an issue as each officer has to buy their own.
I have heard of some people having issues with the Glock 22 and 23s (40 cal models). I've had it explained to me that these frames are basically the same frame as the 9s, and they wear faster due to the increased pressure of that round. Again, just something I've been told but can't confirm.
So as to exactly why my department made that decision, I can't give you the specific reasons why, I just remember hearing there was more than one. I'll ask one of the guys who would know and reply when I get the chance to talk to him.
I'd imagine that this article would likely be some of the reasons:
http://www.tactical-life.com/firearms/7-reasons-cops-choose-9mm-40/