You would think two people who had just gotten married would have more romantic and/or personal things to think about than watching the clock and seeing who left when!
I may be in the midst of marital trouble now, but I can remember being a bride. On my wedding day, my thoughts were for my new husband and our future happiness, not keeping notes about who arrived when and how long they stayed.
I think it is very silly and petty to complain because your sister wanted to take her tired and cranky children home after a very long day.
I had a similar situation when my SIL got married. My dd, who was 4 at the time, was the flower girl. The reception was on a boat, and the boat was supposed to cruise around a harbor for three hours after dinner. Well dinner was late, daughter was cranky, hungry, and tired (it was going on 9 pm by this time), and I didn't want to find myself trapped on a boat with a miserable child for three hours. So I politely excused myself from the reception, and took dd back to the hotel. It was an uproar. How dare I take a member of the wedding party away in the middle of the reception! The bride wanted a picture of her little flower girl dancing with the groom.
Get a grip, folks. Weddings should be about celebrating happiness and love, not toting up a list of who did what for whom and who followed what rules, or posing for pretty pictures, or bringing some fantasy to life. If, at the end of the day, the bride and groom are married, to each other, the wedding has been a success.
If your mom doesn't think so, she can stuff it!