Something to clarify, I'm not really trying to say that people like that want to be evil. People like Shkreli make bad choices not because they like to be bad, but because they're indifferent to the indirect consequences of their choices. I'm extremely skeptical that someone in a position like Shkreli was would be in any serious risk of losing access to essentials like food and shelter if they were to behave more ethically, so I think it's important to set the standard that choosing a job like that when you have alternatives is wrong.
All that being said, I do agree with you that the primary problem by far is the exploitative structure that enables these people to exist in these positions, in the first place. If someone's analysis of the situation ended at Shkreli, I'd encourage them to think deeper. However, I do strongly believe that we don't have to choose between one or the other -- encouraging others to look down on those who choose to be a part of this system can have a significant influence by discouraging others from entering it, themselves. The more voices we have saying "this is not something to aspire to," the more pressure we can build to effect meaningful systemic change.