Last week I called the embassy in Islamabad and was lucky enough to get a visa officer on the phone. Unlike the local staff, the visa officer was very polite and very helpful.
First of all he informed me that the embassy was mistaken in requiring I-797 for a first-time H-4 beneficiary, and that after the FBI fingerprint check (he indicated that the check was only an FP check) , my wife can come in with my I-797 and get a visa.
When I told him that the National Visa Center has already sent the fingerprint results to the embassy, he said that it's a "distinct possibility" that the embassy might not have received them yet, but he said he'll look into it.
A lot of people complain about the Pakistani personnel at the embassy. Some are helpful, some aren't. But I think your chances of getting a fair hearing are increased if you get someone with authority on the phone.