Bostonian here. The Orange Line on the T has been closed for almost a month and that's the havoc you've been hearing about. Fortunately, it is due to reopen on Sept 19 so hopefully the chaos is long gone by the time you visit. There's also some closures on the Green Line but in the Somerville/Cambridge area, not the area near the MFA.
The Silver Line buses from the cruise terminal end at South Station. The Aquarium is not on the Silver Line but has it's own stop on the Blue Line. It's also just a few blocks from the State stop on the Orange Line. Going from South Station to the Aquarium stop would entail transferring to the Red Line, then the Orange Line, then the Blue line - and going one stop each. You could also get off at State (Red, then Orange) and walk a few blocks or just walk from South Station for about 15 minutes. Its a nice walk along the harbor or the greenway.
Harvard would be super easy from South Station. Just take the Red Line towards Alewife and get off at the Harvard stop.
Bonus tip: the Custom House Tower observation deck. The Custom House is one of the most iconic buildings in Boston but it's now a Marriott Vacation Club Resort. Fortunately, they let the public go up to the observation deck once a day at 2:00, except on Fridays. Last time I went, it was less than $10 and they donate the proceeds to charity (Children's Hospital last I heard). The views of the harbor are amazing and it's only a block from Quincy Market. Since COVID, I think you have to call and reserve a spot -617-310–6300.
Enjoy your day in Boston!