A great place to start looking at this whispering you refer to is in Book II Chapter 15, which describes the wineshop before the Revolution and the kind of activity that went on there. Notice the reference to whispering that is included in the description Dickens gives us:
There had been more of early brooding than drinking; for, many men had listened and whispered and slunk about there from the time of the opening of the door, who could not have laid a piece of money on the counter to save their souls. These were to the full as interested in the place, however, as if they could have commanded whole barrels of wine; and they glided from seat to seat, and from corner to corner, swallowing talk in lieu of drink, with greedy looks.
The men who come to the wineshop are too poor to buy drink, yet take up conversation as though it were wine and sup on that instead. The coupling of the word "whispered" with the verb "slunk" indicates that there is something secretive and disclosed about the precise nature of these whispers that speaks of a simmering intensity that only raises the tension in the novel. As we read the entire story, we come to understand that these figures, too poor to be able to buy a glass of wine, are using the wineshop as the centre of the rebellion, and the whispers they communicate are actually planning how and when the revolution will occur. These whispers are therefore intimately connected to the theme of violence and oppression, as the whispers are initially the peasants' first response to the violence and oppression they experience, before they get to practise their own violence and oppression.