I don't know the whole story, but I have known very good, moral people who worked for companies that they didn't completely agree with ethically because they put their family or their health first. Ethics isn't always so simple. If "a very good salary and benefits" is the difference between being very sick or getting that surgery you need, or if it's the difference between sending your kids to a good school or a bad one.... Let's just say that I wouldn't be so quick to judge.
I completely agree with you and don't think you can just call a person 'bad' for working at a 'bad' company. But technically speaking, a lot, if not most, of the 'very good, moral' people you described don't leave the companies even when they are in a more stable and comfortable situation.
Not sure what country you live in but in US and UK it wouldn't be legal to discriminate on a job applicant because they previously worked for in a military-related employer.
I know what you're saying, but as big proponent for anti-discrimination in the work place I fear statements like yours settle in the backs of people's minds and then re-appear the day they find themselves in a hiring position.
