I can see both sides here OP.
If they are childhood besties then I would be slightly offended that she didn't want to stay for the entire day given she has childcare offered to her for the night or could even bring the baby to the wedding. It is ONE day, your sisters special day and she should want to be part of it etc.
However...3 months is still very young and I wouldn't have left mine all night either, mine were still waking for night feeds and would only settle for me or hubby. Weddings can be pretty tiring, especially for a sleep deprived mother to a young baby and toddler, so maybe she is thinking she would be shattered herself by then anyway. Can you imagine staying at a wedding until midnight like everyone else then having to get up several times in the night and probably having to be up ready to start the day at ridiculous o-clock?!
She might love the idea of having a day/evening out childfree but the reality is different, when you have children your priorities have to change and they come first.
If I was her I would personally have asked parents to have the children until the end of the meal and have them drop them to me, fed, bathed etc and with the pram so you can stay for the party bit! 3 year old would enjoy the dancing and baby could sleep in the pram, win win! But everyones situation is different of course and this may not be feasible.
I think your sister needs to be more understanding maybe and not take it to heart. She will be having the best day ever and like a pp said, probably won't even notice she is gone! Just get on and look forward to the day without worrying about it, planning a wedding is hard work and in the grand scheme of things this really isn't anything to spend time worrying about!