Great question Lisa. I took an ethics class in college and it was fascinating. I went to a catholic univ and our professor was a priest so the debating got really intense at times.
Taking tainted money in the ways you described is no different than making money from advertisers who's company's stand for greed and unhealthy things. I've seen a lot of those around here that make me cringe and even though I know the money from those ad banners pay to maintain our site it bothers me on such a deep level but I continue writing here. Some examples because I know how inquisitive you are:
Here at bellaonline:
Sketchers shape ups - I hate what they stand for and the fact that their spokesperson is a complete brainless bimbo makes it that much worst.
RIFT - promoting our youth to sit for hours playing violent video games (I could write volumes on how I can't stand video game culture but don't worry I won't).
On my site freeworkoutsguide.com:
Jillian Michaels - I think we all know how I despise the B.S. Loser approach to fitness (shame, torture, babysitting and drama) not to mention that people sit and watch the show and feel all great about themselves for vicariously "exercising" with those losers but they hardly get any real exercise (sorry for the rant). Real fitness is nothing like that stupid show but I let Jillian pay my bills!
Med shape, Herbal body wraps, crossfit, are others that I make money from and can't stand. I could easily block these ads but why. I need to make money from spreading my message too and my readers, the ones that truly care about their health, won't click those ads. Those who do aren't the kind of readers I want on my site anyway. Like I said in my other post it's not my job to convince you of anything only to guide you if you are ready to change.
The situations you brought up are different but not really. I'm sure we've all gotten our fair share of tainted money especially those of us who have worked in the service industry. If an advertiser who I knew was running a child pornography ring offered money to put ads on my site I would say no but what are the chances that you'll ever know that.
Bill Gates donates billions to Big Pharma and Biotech so they can continue making people sick. Will you stop buying his products? As with many things in life ethics is never as clear cut as you think.