Therefore, can an Auditor question the decision taken by the Top Management to approve deviation?
Hallelujah...Yes, we can....
Finally some evidence of an auditor with enough courage to burst top management's dictatorial tendencies. Obviously, I am making a number of assumptions here, but all too often top management will disregard performance requirements, safety issues, validation and verification decisions, etc. and use their "authority" to shove/rush an underdeveloped product into the market, simply for financial reasons. Pressed by corporate to improve their bottom line, some misguided "managers" will make decisions against all the data, putting the organization, it's employees, it's customers and it's future at risk.
I am extremely impressed and surprised that your external auditor was brave enough to call your top management's bad decision. It is a very rare occurrence. Most external auditors spend their time with document control clerks, calibration supervisors and don't have the guts, knowledge or competence to interact with and challenge "top management".
Tell us more....