Of course Shkreli's arrest further hampers the reputation of big pharma. Any time an arrest occurs, the reputation of the individual is hampered and so is the reputation, in this case, of big pharma. The concept of 'guild by association' comes in to play and rings true in this case.
Shkreli's arrest further hampers the reputation of big pharma because it is clear that yet another one of the people leading it is corrupt. His arrest on the charges of fraud demonstrates that he is not an adequate leader of any company, especially a pharmaceutical company that people rely on for life-saving medications. Shkreli is yet another bad example of the greed that runs big pharma.
I think it's possible that this would further damage big pharma's reputation, but I really think this more an issue about a solo man. He has made headlines for his deplorable decision, and I think he has gone much further than other companies would dare to. I don't believe his arrest is really going to hurt the industry.
The arrest has nothing to do with the Pharmaceuticals industry. The arrest has to do with financial fraud, which has nothing to do with the pharmaceuticals industry. The damage to the Pharmaceuticals industry's reputation was already done through notorious actions taken already by Shkreli and other firms. So, no the arrest won't further hamper the reputation of the Pharmaceuticals industry.