Regardless of whether Shapiro is biased, or thought of as biased, it is really irrelevant to the situation Harper and Emerson have created for themselves in the eyes of the public. First of all, Harper set for himself and the CPC a higher standard of behaviour than other political parties. Immediately upon election, he is seen to have abandoned this standard by choosing Emerson and Fortier.
Emerson defects to the CPC barely hours after his election. How does that look? It looks like patronage, regardless of anything else, that's what it LOOKS like.
Now the ethics commissioner - empowered by parliament - announces an investigation and Harper declares he will not cooperate. How does that look? It looks like a petulant prime minister with something to hide; a prime minister who has abandoned his "higher standards" of conduct and become just another sleezy politician.
It really doesn't matter what happens to Shapiro or what anyone thinks of him, Harper's arrogant response to the situation as a whole has damaged himself and the CPC.