As I understand it, the reason that municipalities are prohibiting storm water discharges from gutters, etc. into the sewer is to prevent "combined sewer overflow" ("CSO") events.
Sewers can be combined (sewage and storm water winding up in the same pipes) or separated (sewage and storm water carried in separate lines). The problem with combined sewers is that all the pipes eventually lead to the water treatment plant. The plant is only designed to handle a certain amount of flow. In the event that there is a heavy rain, more volume has been added to the flow than the treatment plant can handle. When this happens, flow is diverted away from the treatment plant and directly into a body of water. This is a combined sewer overflow. Obviously, CSOs release raw, untreated sewage into waterways.
Portland has had a problem with this over the course of the last 20 years or so. So have many older cities. The EPA frowns on CSOs and raw sewage discharge into waterways. Making homeowners separate their gutter system from the combined sewer reduces the frequency and intensity of CSOs.
Here is a link to a wikipedia page explaining CSOs better than I can:
Combined sewer - Wikipedia, the free encyclopedia