Bad/spam sites irrespective of whether they are directories or not are banned from google/other search engine indexes/results Not 'all' directory sites are banned.. So it make sense to run quality directories.
General directories that are not reviewing sites and clearly just in it for the money are not liked much by google. They get penalised not banned. Niche directories and directories accepting useful sites who are building their site for the end user, not the webmaster are not hated by google. People build directories for money, to expand their current site, or as a hobby.
I think you mean penalised when you say banned, theres very few banned. The idea of building a directory now? for whatever you want it to serve.
google is crazy and look stupid. no idea why my free web directory would get penalty and was dropped pr from 3 to nothing.
also my directory qatelier.com was pr4 and after last update got 0 pr, but now seems the traffic is higher, i don't know why..
if you are building a quality and informative directory site, i dont think google will banned you. those that were banned are mostly built for money purpose or just a crappy directories which deserve to be banned. good directory always welcome by google. think about money as the second purpose and you will be fine.