I just noticed that if you put things in different programs, then it is possible to duplicate folder names. That would have been nice to know. It solves my problem for now. The downside is that you cannot put programs in programs, and because of that the program itself cannot have duplicate names (So they have to be named Adwords US, Adwords UK etc)
the Standard version of marketo allows separate work spaces for different departments. Would this offer a solution?
no it would not. Folder names have to be unique even across work spaces.
If you consider upgrading to use work spaces, I'd suggest to think about that very carefully. We are using work spaces, but from my point of view the disadvantages outweigh the advantages.