Really I think this mostly boils down to IC consequences - if there are some that will make the characters comply with the new housing situation, then I'm fine with them being shuffled around.

Tess, for instance, would be fine living in separate housing as long as she's close by - she'd be concerned if Joel were, for instance, forced to choose between Sarah and Ellie because she thinks that could have negative psychological ramifications on him. She would, however, grudgingly comply with, say, an imposed kind of martial law situation where they are now assigned housing and would face fines or jail time for non-compliance.