A non-codex chapter will find a harder time of getting enough allies to 'pull a Badab'. Huron got away with it because the Claws were already in the Maelstrom Warders union of chapters, and he could call on the Executioners' oath.
The vast majority of chapters from second founding onwards are Codex chapters from Ultramarines stock, because the High Lords favor this.
But essentially, Imperial law operates in trial by combat. There are too many figures who are empowered as the Emperor's proxies- Governors, Inquisitors, and Chapter Masters among them. An Arbites Judge can call on the same authority, so can a Cardinal. Whenever figures of such power disagree, it comes down to who has more guns and bigger, and usually this means the Space Marines get left alone.
But an Inquisitor could always commandeer an Imperial army, or have chapters indebted to him to call upon. A Judge could levy a task force of Arbitrators from across the sector, and Arbitrators are some serious business. They have their own ships, too, apparently. A Cardinal can declare a War of Faith and suddenly Frateris Militia everywhere. A Chapter Master has his own chapter and that's enough. A Governor has the loyalty of his homeworld (one hopes) and a tremendous amount of wealth.
The Imperium stays stable because everyone has a gun to their head.
Or, actually, because nobody knows if there are guns on their head, or how many.