First, what did you answer when the auditor asked you why you hadn't audited sub-processes? I thought your rationale included here was acceptable--there are so many it would be unreasonable to review them all. Perhaps though, a sampling from one of the five main processes would be appropriate. The choice of process for which a lower-level sampling would be reviewed might change periodically, or every x audits, or based on some other indicator of priority. In support of the auditor's perspective, if you never get to the lower-level processes how do you know they are conforming? It is often the case, especially in older, more established operations, that gaps exist between what is written and what is actually being done. Thus, even when the output is conforming--suggesting that the process itself must be conforming--there might still be hidden efforts being made to make it so. Also, and in the spirit of continuous improvement, if you don't dive into the details how will you know what needs to improve? I appreciate your position. Keep the faith.
1. Sit down with the process owner of each of the five major processes and ask them which would have the most impact on performance (customers, product, cost, etc.) if they failed.
2. Look at performance data (e.g., customer feedback, complaints, nonconforming material, delivery performance, equipment downtime, ...) to identify which processes may be having most difficulties. Review corrective actions to see what processes were involved in the nonconformity.
Also, consider that you can also not just audit for compliance, but also to look for opportunities to improve. You could have process owners/subowners participate in these audits as observers and discuss what you see. Can use a lean perspective, quality defect perspective, ...