Oh, I know that the Secretary of State is not (officially) a civil servant. Both are indeed part of government. But as you rightly point out, the person that they do get to independently assess this is overwhelmingly likely to agree to whatever the executive wants: it will be a rubber stamp and thus an approval in all but name from the Secretary of State. I very much doubt that if you found yourself in that job saying 'no' a lot, you'd be in a position to keep it for much longer.