Not that situation specifically, but there were times when my MIL would make decisons that I didn't really care for, so I took away the ability for her to NEED to do that by controlling what I or the kids did prior to going to her house...whether it was making sure they were full and didn't get fast food while they were there, etc. or makign sure that they knew that mom still had rules even though they were at grandma's.
It sounds like your SIL is "my way and I don't care what mom has to say" about all of this, which makes it a little more difficult, especially if your ex isn't willing to at least partially work with you on this one. Why he can't tell her, 'You don't need to wash their hair...' is beyond me.
Anyways, i think that in order to avoid confrontation with him or with her, telling him they get home too late is probably the way to go. Especially since it's a Sunday, you can always also blame it on needing to get ready for school Monday, etc. It just makes it easier for everyone/they get a chance to be home and get settled, etc. You realyl could use almost any 'reason' for them needing to be home earlier.
I think I'd also fear your SIL screwing up your daughters hair to the point where it is damaged and costs $$ to try and fix...and she'd likely not help much if you needed to take your daughter to a salon or something, KWIM?