The Three Great Powers, composed of the Marine Headquarters, the Seven Warlords of the Sea, and the Four Emperors, are the three greatest military forces on the oceans, and their relations are very vital to the World Government. The three powers exist in a delicate balance of power, not all the details of which are known. It is however known that only the other two organizations are equivalent to the Four Emperors.
Considering that these organizations are stated to be a balance and the fact that the loss of Crocodile threatened the balance, it is likely they are approximately equivalent in strength. The Emperors and Marines seem to be on the opposite ends of the spectrum, with the Marines being more orderly compared to the Four Emperors which are very chaotic, with the Seven Warlords acting as somewhere in between.
The Gorosei fear that if this balance gets disrupted, the world itself could descend into anarchy, and the balance itself appears to be very fragile as the loss of even one key member (such as a Warlord) can disrupt the balance. This is why the defeat of Crocodile was so distressing to them; the loss of such a powerful ally in such a public manner tips the balance away from the Seven Warlords and in turn the Marines. This leaves them with diminished force to counter the menace of the Four Emperors and allows the general populace to question their power and authority. Another concern is that the Marines are the sole organization completely under the supremacy of the World Government. The Seven Warlords of the Sea often follow orders on a whim, if at all, and the Four Emperors are entirely outside of the World Government's control.
As the delicate balance of the Three Great Powers is what stabilizes the world, the existence and actions of the Revolutionary Army is a threat to that balance.