"If a top guy says the parents are covering up the death then why argue it"
Are you blindly accepting the Portuguese ex-detective is correct and that the McCann's covered up their daughter's death? Really?
If you apply even a tiny bit of common sense even you will be able to draw the conclusion that the ex-detectives comments don't stand-up to much scrutiny.
There was a moron on this site sometime ago (I can't be bothered to remember its name) who seriously suggested they drugged her but administered too much and killed her. Idiocy doesn't even begin to cover a comment like that. If it genuinely believed its comment, then I'd love them to explain what the McCanns did with the body that has managed to baffle the police.
Anyway, to the question - Yes, if the McCann's are required to have to pay costs, and there's nothing to stop them using the fund, then I think the sum should be paid for from the fund. They have a right to challenge the despicable comments, and for a couple who have experienced every parents worse nightmare, to have these allegations levelled at them is rubbing salt into an already open wound, so saying they should fund it themselves is a pretty sh11ty thing to want.