You have to first find out if this chap's father has disappeared due to some other reasons and there is no government involvement (as Pakistan is a lawless country and many Pakistani disappears regularly). Further, if he is really in custody than we have to find out that why he is in custody and where he is in custody. It is possible that he is a local terrorist in custody of Pakistani security institution (something justifiable) or he is terrorist caught in Afghanistan and is with American authority (that is fine too).
I believe (though that is speculation and I might be wrong) that he might be in custody of Pakistani security because of his links with terrorists and traitors fighting state (Pakistan) and thus his custody is justified. Anyhow, this type of disappearance without letting family members know his whereabouts is maybe wrong for countries in peaceful time, but acceptable for a low resource country like Pakistan, especially when country is fighting a war within country for safety of the country, as there are number of traitors and terrorists fighting state (Pakistan) who do not accept the writ of Pakistani government and are working against Pakistan as traitors.
Why was Musharraf reluctant to release information on whereabouts of the 400+ people? Why did Mush not declare the list of detained people? If any Pakistani was deemed terrorist he must've been prosecuted in Pakistan before handing out to USA for $5000 (or whatever the amount was).
Being a major donor doesn't give you right to kick your behind or cut your limbs.