Will Boston have to build Facilities to accommodate the olympics to only have them go into terrible disrepair because no one uses them?
They don't have to let stadiums fall into disrepair, they could build a stadium that can be developed for multiple use, for example moving the Revolution into the stadium and away from the hell hole of foxborough or have BC use it. There are plenty of preexisting venues, they probably need a velodrome and an aquatics centre.
If you want to do the games efficiently it can be done. Glasgow held the Commonwealth Games, smaller in scale and missing a few events but an existing stadium was refitted, a swimming centre and a sports multiplex (which included a velodrome) which the city needed regardless and an athletes village built to regenerate a deprived area. Everything will be used for decades to come.
London is doing ok with keeping their infrastructure going even if it cost too much. What you don't want to do is an Athens Olympics where they built everything way out of the city and have it fall into disuse. There are plenty of colleges that can make good use of facilities in Boston.
The main thing that will cause overspending is consultant firms, management firms and security where the contracts seem to go people friendly with organising committee.