The essence of the ISA program is for retailers to have someone on their team who is trained in PCI nuances and who can help the chain maintain compliance between assessments. Most of the retailers that are working with the ISA program plan to continue using their QSA. If ISA works, it would enable much faster and less painful assessments, because someone internal at the merchant is constantly watching for anything that could cause a compliance problem.
To be candid, none of the players involved is independent at all. The internal folk are all on the retailer's payroll, and the external QSAs are all being paid by the chain to conduct the assessments. What keeps everyone honest—more or less—is the overall infrastructure. Between the banks and the card brands and the QSAs and—for publicly held chains—shareholder attorneys, there's simply not that much opportunity for anyone in an ISA role to get away with much.
After all, their prime function is to make the assessments go more quickly.
This gets us back to the auditor question. Given the infrastructure surrounding it, an auditor is an excellent choice. But if the auditors are busy with 40 other projects and a mid-level IT security manager is available, why not go for it? It doesn't make a lot of sense for MasterCard—which originally pushed for an auditor for more independence, but which now seems to have backed off—or the PCI Council to insist on an auditor. If the senior person at the chain wants to use a non-auditor, there's not much reason to object. If the non-auditor ISA doesn't end up accelerating the assessments, the boss will have just wasted her own time. But it's her time to waste.
The practical fact of the matter is that the vast majority of the people who work in the security arena on a retailer's payroll care very deeply about security and will function well for their chain. The training of an auditor is helpful, but I have to side with the Council on this one. It's a nice to have, but hardly essential. At least for this specific program.