I think we can tell the difference by looking at the claiming transactions. However, Alitin has a real problem here going forward. They will need to try to differentiate between the people that got ripped off by having their BTC swept by the thief and the people trying to rip them off by reclaiming the BTC themselves and them filing a claim.
You're presuming that Alitin is planning to reimburse owners for the theft, I've not seen or read any such intention. The statement provided by the Alitin guys here is a deep, sincere apology and an admission that they've initiated an investigation on the matter and themselves.
The company is out of business, what claim is to be made?
The best way for those that got robbed to recoup their loss is to file a claim with their insurance company (i.e, homeowner's, renter's). These coins are collectible and have value as currency and art does...they would be covered by any basic insurance policy for personal possessions.
So sorry to hear of everyone's loss. We all lose in this situation, if not by monetary means by the mark down on the reputation that bitcoin and physical cryptocurrency has been working hard to build. A crime against one is a crime against us all!
I will call my insurance company but I expect there is no claim unless they were listed on a special rider. I have artwork (paintings) and had to insure them separately. I did not do that with these coins, but it does not hurt to try the insurance path.