Congrats man! The nice thing about choosing between Harvard and MIT is that there are so many things in common between them (location, prestige, and quality of training). I applied to the Biology PhD, not to Microbiology, so there may be some differences in our experiences.
Personally, I only applied to rotation based programs as I'm not entirely sure what specific research topic I'd like to pursue. When I was deciding between programs, MIT stood out to me in a big way due to the fact that they front load the coursework in the first semester. From what students have told me, it really helps to build a strong knowledge foundation, foster cohort camaraderie, and let you focus more on choosing the right lab in the spring. Personally, I think that this will let me have an easier transition into grad school as I haven't taken any classes in the past 2 years.
The shorter rotation times (4wks vs 8-10wks at other programs) also appealed to me as I think that this system really emphasizes the fact that you should spend the time focusing on fit rather than trying to complete a small project. If I don't mesh well with a lab, I definitely would not want to be stuck there for longer than necessary, and I think that fit can be well-determined during the course of a month.
While there are a lot of opportunities for industry work, I definitely didn't get the sense that the program was biased in any way. I think that the program provides a lot of support and training whether you decide to pursue industry or academic work after the PhD.
Are you worried that the lab at Harvard will not work out? Is it relatively easy to find a new adviser if things go south? In the end, it's the mentor that matters, but I personally wouldn't feel comfortable without having at least 2-3 potential advisers in a program.
Either way I don't think there is a wrong choice here. See you in Cambridge/Boston!