First, just because all versions of cytochrome C do basically the same job, it does not follow that there are no functional differences between them. For example (based on zero knowledge of the details of this particular protein), two versions might function best at two different temperatures. So more than drift might be involved -- but most of the observed differences probably are due to drift.
So if they are functionally different and even some differences are not due to neutral drift, can Cytochrome C be used as evidence for common descent?
I don't understand what the issue is here? Could you explain what the perceived problem is?