If the Maquis could attack and disable the Malinche
without murdering its crew, then they could have done the same to the Bok'Nor.
But then, they wouldn't get to kill Cardassians, would they?
And let's not forget that it was Eddington who came up with the plan to use biological weapons AGAINST CARDASSIA ITSELF. Of course, the plan was a ruse, but the fact that Eddington came up with it at all was rather telling. If he could have actually managed to get it to work, I'm sure he would have. Perhaps not all Maquis commanders would have done it (Chakotay, for example), but Eddington definitely would have.
Part of the problem, then, is that the very nature of the Maquis as a radical revolutionary movement - with no central authority or leader - means that the possibility of some random psycho coming up and committing crimes in the Maquis name becomes more of a risk. For every 'noble' Maquis like Chakotay, Cal Hudson, or even Ro Laren, there's people like Eddington, Lon Suder, etc.