The minister's input into the overall evaluation of a deputy minister is one input among many. Ultimately the Clerk of the Privy Council advises the Prime Minister on the assessment of the deputies and will convey the views of the minister but will also comment on whether that's justified in the circumstances, whether that's a fair assessment.
I think you're alluding to a case where there is an improper attempt by the minister to influence, or to intimidate, or to get back at a deputy. That seems to be the hypothesis of your question. In that case, the clerk, in advising the Prime Minister, is in a position to say, well, the minister says this; however, take into consideration the following matter as well, to balance it out. The minister's input is but one.
Under our system of responsible government, it would be difficult not to get the minister's input. I think you need the minister's input into the assessment of how that deputy minister is performing. Absent that input, you would have an incomplete picture.