Thing is the Guises are Politiques at this point--they DON'T want to smash the Protestants right now. (Also, their rivalry with their cousins the Bourbons isn't so bad right--the real people they have a hate-on for is the Montmorencys.) This is a BIG problem for Henri's little anti-Huguenot crusade--there's not a lot of enthusiasm at the top for it at this time. The three big families of his reign--the Montmorencys, the Bourbons, AND the Guises--all aren't very keen on it. The courts and jurists aren't very keen on it either. It's basically Henri, and a few very old courtiers he leans on, one of whom is his mistress. (Not that there isn't anti-Huguenot sentiment, but it's a bit lower down.)
Were the Guises really Politiques, though? The term it's self didn't even gain currency until the Catholic League was founded. Which yes, it was founded by Henry, Duke of Guise, but he was the son of Francis (1519 - 1563) which is the Duke of Guise we're speaking about and who was paramount during Henri II's reign.
He was universally popular, affable, and France's premier military figure. Yes, there was a lot of dislike of the Montmorency's too, just as the Bourbons, but I think it's a little wrong to paint him in the shade that he has a politique. He seemed to have no issue of Henri II's use of the Burning Chamber. The Bourbons were, and you're right, a practical nonentity at this point, although it was Henri II who rose them up a bit more by arranging that Jeanne d'Albret, his relation, marry the Duke of Bourbon. In fact, the big issue Montmorency had with the Guises were that they had supplanted him as the keys key advisors. Considering he readily allied with them against the Bourbons (perhaps more "the enemy of my enemy is my friend). The family feud definitely continued under his sons, though.
In the scenario of Henri II living, Montmorency still has his honors, but is still supplanted by the Guises. There will definitely be issues with that. I'm still not buying the Guises as politiques though -- not that I don't believe you, but most literature points to Ultra-Catholic affiliation. Although Henri II's death only cemented the Duke and Cardinal de Guise's supremacy on the council, they were a strong influence even before that, as Henri II was pretty weakwilled and greatly relied upon others.
The Cardinal of Guise is a true enigma and could have been a politique, but I hardly see it: approving of the Augsburg confession is one thing, but then wanting to establish the
inquisition in France? He was definitely a torn man, but the Guises were oppurtunists above all. The Catholic Party didn't exist yet, but I would hardly say they were too upset of Henri II's intense bigotry. They probably thought it a waste of time and better to quash or appease the movement in Scotland and secure their niece's inheritance for both her and her husband the Dauphin before settling things in France.
Less politiques, and more opportunists, and great masters of the policy of the carrot and stick. Without Henri's death and the tumult of Amboise, their views won't radicalize. In such a case then, I do agree that they would urge Henry against being so ruthless in this case. Quash the smaller bug in Scotland, then crush the bug in France.