Depends on why you're eating the liver. If you're wanting to minimize your dependence on nutritional supplements then bang for the buck's a lot better with liver than with some other foods. For instance, you can pretty much get your choline or vitamin A requirement for the day (in the latter case, for something like half the week).
FWIW, I haven't gone through every single nutrient, but there are pages available on the USDA site that tell you the best food sources of certain micronutrients. Of the pages I've looked at, it's not very common for chicken liver to come out ahead of beef liver on something. (I've seen turkey innards rank pretty high but not usually chicken.) And it's worth noting that chickens are nearly always confined for their entire lives in a CAFO setting, but with beef cattle, most of the CAFO stuff comes in the last few weeks when they're being finished. They still spend most of their lives on pasture, whereas your average CAFO chicken never leaves the warehouse or the cage.
So in the aggregate I'd still go for the beef liver, even if it's CAFO. And I'm not convinced the drawbacks of whatever might still be in the liver would outweigh the benefits of eating it. Your mileage may vary unless someone comes out with a definitive study.