Again to clarify my biases: I am a white male non-Mormon, non-software developer. I want to address three of the most common complaints and give my view.
Non-monetary benefits - There has been a lot of complaints about things like parking and paternity leave and a lack of free lunch trainings. Many of the people working at Clearwater have very little career experience elsewhere. The benefits that are provided are quite generous compared to other companies I have worked for. The point is that this is a comparison problem. When compared to Google or Amazon the benefits are light, but in the local job market they are adequate.
Pay for non-software developers - exacerbating the previous issue, many people feel under paid. Whenever you are in a company where there is a large distinction between two groups, in this case the software development staff and the rest of the company, it breeds resentment and angst. Most people are happy to take the job initially and, assuming they perform well, receive salary increases of greater than inflation each year. However, comparison with those they work with makes it difficult to accept. You can make good money at Clearwater even if you are not a software developer but if you want to make as much or more than all your co-workers, get a computer science degree.
Discrimination - the two most often cited are religion and gender. I will not try to speak to gender since I am not of the gender considered discriminated against. I will only say that, on the teams I have been a part of, females have been hired, advanced, and I have had female superiors. On the religious front, I think I can speak to the issue. Let's be clear, all of the upper most management is Mormon. However, there are lower level managers that are not and I have never felt it has been used against me. All of the top level management was internally sourced. Tenure and merit seem to be in line with those promotions.