The worst outcome of this isn't necessarily that Boston got locked down, although that's definitely worth discussing.
The worst outcome is that lockdowns are becoming more and more common, far out of proportion to the actual risk. Once it becomes normal to lock down an entire city in response to a very real and significant threat, it then becomes much easier to feel normal about it when we lock down an entire college campus because a mentally ill homeless person made some faculty or staff uncomfortable. It becomes normal to do what some community colleges in my area are doing, which is to have an active shooter drill once a year in which adult college students are locked in a dark room for 30 minutes and told they can't leave. (This passive response is, BTW, not at all in line with what experts recommend in such a situation.)
Destroying 30 minutes of instruction for a whole campus and violating students' civil rights is way out of proportion to the risk of getting killed by an active shooter, which for a college student is on the order of 1 in 300,000 per year. A college student's risk of being a victim of rape, robbery, or assault is about 1 in 100 per year, but we're uncomfortable dealing with that -- in fact, there is a wave of lawsuits right now by women who say their rights were violated when their colleges refused to take action about their being raped.
To use an analogy suggested by Scheneier, active shooters and the marathon bombing are like shark attacks, and other violent crimes are like dog bites. The number of people killed by dogs every year is much, much greater than the number killed by sharks. But we find shark attacks much more psychologically compelling.