It is most unfortunate that this should happen to you.
5 days for a non-immediate relative is quite generous, but if that is what the guidance says, then that's what it said. When I 've been on the other end of this (deciding whether to grant compassionate days outside guideleines), we try to sensitively find out the closeness of the relative involved and the amount of work being done by the family member (making all the arrangements or just a bit-player). On this one, I'd have asked whether there was anyone on the husband's side of the family.
That is irrelevant now - as the days have been taken.
For 5 days pay and the possibility of associated negative publicity with other employees, I think it unlikely that the company would make a formal legal issue of it.
I would just go back and say that you took the time in good faith, the manager was aware of what you were doing and given the circumstances you feel it is a little unreasonable for the company to seek a claw-back now.
There is no definitive legal answer to your question 'am I obliged to pay' - as the answer is 'only if a court upholds the company's claim'.