What an unfortunate situation! I agree, I would postpone sleepovers for the foreseeable future (like, at least a year, if not longer) until this gets resolved. It's not so much that anything so terrible happened, as that several strange and dramatic things happened all at once when there were no previous incidents. That needs to be nipped in the bud, and if that means no more kids overnight in the house than your own two, so be it.
This is kind of random, and I hope it's not true because it's creepy, but is there any possibility that it was someone who broke into your house that night? If you and DH and DS were sound asleep on the first floor, and everyone else was down in the basement... I'm thinking, were there any unusual marks on the outside door, mud tracked in, mentally ill homeless people in the neighborhood (scribbling on the counters, dog food in the cheesecake sounds kind of irrational), neighbors who come home drunk and might have opened the wrong door, etc.. I think it's a remote possibility, but since no one else mentioned it, I thought I would, just in case.