Using open source development tools is fine. What matters is what you distribute to end users (i.e. the output of those tools). I think the issue with unity is that VLC ends up being distributed as part of unity applications.

I'm not a lawyer but this might indeed have some valid issues associated with it depending on how this is done. So, I can see an argument for Unity simply not wanting to put their customers in a situation where they have to worry about these issues. It seems a bit drastic though given how useful it is.

Banning companies/accounts seems like it's simply unprofessional/rude and unnecessary. Sounds like they need to have a conversation with whomever thought that was a good idea about professional conduct.