Great questions!
In general I would say: you don’t separate the members, but you separate the content. Like @merefield said in his post, commercial activity could be restricted to a specific Marketplace category for example.
Here on Discourse Meta, we see plenty of people that sell stuff, but they are also very helpful members of our community. Answering questions etc.
This could work, it would really depend on the type of orgs.
In a community I managed before, we had official partners. Those were clearly labeled differently from the “random” implementation people.
Yes, probably.
But the key will be a strong, non-ambiguous (and enforced!) Code of Conduct. Clearly spell out what is and what isn’t allowed. What behaviour is expected and tolerated?
This will depend on what’s in it for everyone.
Here on Meta, we don’t charge others. We believe that they make the overall Discourse environment stronger. We want many people to use Discourse, our community members help to make that dream a reality 
If you are facilitating the transactions, and not benefiting (indirectly) from those transaction happening.. then yes, maybe you should charge. It all depends on the specifics.