A quick search verifies that it did happen, but I wouldn't trust any article written in the past two years on the details. Wikipedia says he quarantined his troops who showed symptoms, individual households were quarantined and his army made strategic retreats from areas with known outbreaks. There were no lockdowns and the head of the household was legally responsible for anyone in the household who had smallpox getting out. The troops in Boston were to monitor/forcefully quarantine individual households with smallpox.