I guess that is part of the problem of working with family, divided loyalties.
The company may well have been wondering about why your FIL didn't tell the company himself (does he work there too?) and wondering about his loyalty seeing as it came to them second hand.
It could prejudice your relationship with your partner, yes, having potentially dropped his father in it but then I guess it's one of the risks you take on when members of the same family or similar work for the same company, there are potentially conflicting loyalties.
You can't blame the company for them expecting their staff to be loyal to them and report such things, it's not their fault that you have other issues. To them you are members of their staff, the family tie doesn't come into it and why should they make allowances in this kind of context?
I'd be concerned finding out a member of staff knew that something had been stolen by another member of staff and it was not reported.