I don't know how else you push a couple thousand people on a marathon inside of city limits without it almost having to shut down most if not all of the city. I get the fact that it becomes an huge nusance for the residents but they can always move if the one day is that big of a deal.
The Boston Marathon is, and always has been, a big deal for the city, but it certainly isn't the only thing going on in Boston, even on its weekend. There should be a large police presence, as with any big event, but it doesn't mean that stores, parks or other venues need to be closed,
If the entire city enjoys and supports the Boston Marathon, then this would be acceptable. While it is a major event, not everyone enjoys it though. Because of this, their lives and businesses should not be interrupted for even a few hours. Shutting down the city will not help the Marathon at all, and it will just be an inconvenience to those who do not want to take part as a participant or as part of the crowd.
The Boston Marathon, held on Patriots' Day every year, begins 26 miles north-west of the city of Boston. It winds through Boston suburbs and actually only travels on a few miles of Boston roads and streets. To close down the entire city when only a few miles of city streets are used by the race would be unwise and unnecessary.