Over the years, social management systems in games like this have often seemed weaker to me than other parts of a game. SoIFRP has a fairly robust system, though which I find if you treat it like combat can have good results no matter the disparity between 'levels' of the participants in an Intrigue.
A key point I find useful to remember is that in most cases involving dialogue and interaction, no one leaves unaffected. Keeping the human reaction to what is going on in the forefront of your mind as GM during each stage of the scene, whether it be manipulation, seduction, persuasion, intimidation or what-have-you, helps keep things on an even keel. By running the intrigue with the idea that at the very least they will walk away from this with something to say about their opponent's statements or reaction ("What an idiot!" or "How clever!" and so on) no matter the outcome, they will always have some weight.
In the specific case you present, the characters are highly adept at this sort of thing and should be rightly feared as persuasive men and women. As the GM, you have discovered that they can get what they want from people easily. The challenge doesn't really lie in letting them use these abilities or in changing the system to reduce their effectiveness, it lies in making the use of them interesting for everyone and allowing the NPCs to react as they would.
- Bring Allies: If entering negotiations with the PCs, give the NPCs the opportunity to forge alliances and connections with other NPCs who will back them up and balance out the encounter, providing them with improved ratings and giving them a chance to recoup composure (Assist, Manpulate, Mollify,Read Target). The idea here is not to prevent the PCs from being effective, but to keep the Intrigue interesting, give it nuances and challenges, and have it have broader effects on the game.
- Layer the approach to the people with decision-making ability: Create defensive buffers of retainers and officious windbags between these social warships your players have created. Make them work for what they want and in so doing provide an ongoing stream of hooks, rumuors, and supposition for both the players and the NPC community to work with as a result.
- Attach Conditions: Create webs of inter-related promises and commitments which persuasion alone will not be able to overcome. While the target may earnestly want to yield to the characters, they simply cannot roll over without dealing with agreements that have already been put into place. These conditions will have the bonus side effect of causing chain reactions of events if altered to benefit the PCs and both good and ill may rise from that. Additionally, nothing comes for nothing, and a person being strung along on empty promises will run out of string eventually.
- Avoidance: No one likes to be manipulated or made to feel like a tool. If the characters do not work to maintain good will among those they are verbally pushing around, it should not be assumed that the attitude of the NPCs toward them remains cordial. As relationships deepen even good friends may come to say, "What have you done for me lately?" Situational modifiers based on the results of past Intrigues, plus the reputation of the PCs, plus the desire to simply never get into a room alone with them can all add a level of realism and challenge to the PCs quest to get what they want.
- Go to War: Having Intrigue devolve into combat is a problem and unsatifying, to boot. However, as the PCs run roughshod over the balance of power, someone somewhere will get their feathers ruffled enough to commit troops to the field if things tilt too far in any particular direction. Let them.... and let the Kingdom know who is to blame.
Ultimately, as it states in the question, the PCs were designed to be social intrigue powerhouses. The game will have to allow them to be so, but it does not have to just lie down and take whatever they dish out. Use the system to challenge them, extract conditions and leverage from them, have the NPCs react naturally, band together, and seek help, and remember with sharp detail all the promises they have heard before.