I think you hit the nail on the head, while protection is needed, it is overkill, and the fact that what happened last year was tragic, the groups that might think about doing something will not utilize the same method as they know it will looked for and prepared for as well.
Also the fact that it is published, they will look for another way to do something if the marathon is determined to be a target and with all the security and upgrade of searches and protection, it is now considered a "hard" target, which gives them a reason to look for a "soft" target with all the police and protection pulled to the marathon, many other important targets in Boston could become prime choices, that is something that the powers that be need to also focus on as well.