I think that when Moffat leaves he'll bookend the River Song stuff so that the next Executive Producer doesn't have to write another River Song story.
Maybe the crying is partially due to eleven knowing that he is dying. The towers singing could be another "Vale Decem" moment.
The last time I saw you- the real you, the future you, I mean- you turned up on my doorstep with a new haircut and a suit. You took me to Verilian to see the singing towers. What a night that was. The towers sang and you cried. You wouldn't tell me why, but I suppose you knew it was time. My time. Time to come to the Library. You even gave me your screwdriver. That should have been a clue. There's nothing you can do.
Maybe the crying is partially due to eleven knowing that he is dying. The towers singing could be another "Vale Decem" moment.