You shouldn't need to worry about the vibrations. If you are really concerned, just use it on 2 or 3, rather than 6, then you can speed up once you feel comfortable with it.
The real concern you should have is harming the "plastic film" on the window. Auto safety glass is made to break into lots of little pieces, rather than large "spears" so as to be more safe in crashes (less death after impact). As well, the glass is sandwiched between two layers of film that help to contain the glass. If you get too aggressive with a compound, you could easily go through the film.
As well, glass has to be fairly free of irregularities/distortion. If you polish one area too much, you could cause a "warp" in the field of vision.
Just some words of caution. If you really want to work at it, I'd recommend seeing a professional and asking if they could fix it. If they say "No", you've saved yourself some time and aggravation. If they say "yes," consider if their quote would be worth more or less than your effert. If too high, then at least you know that you might be able to do something with it.
