The last part of that article was the only worthwhile part, IMO. Treat everyone the same.
I wouldn't worry about de facto discrimination , unless I was at a large scale level, and then a more nuanced policy looking at types of convictions would be warranted. Even then, one could argue de facto discrimination (as, say, homicides is likely disproportionate by race, or gang activity, or whatever). But again, as the article notes, safety reasons are a legitimate concern.
Follow the advice at the end, and all other fair housing practices. I wouldn't suddenly change my screening practices because of this initial warning from HUD.
This was good to know (where things may be shifting) though, so thanks for the link! :)