If this were a very minor subplot, contrasting Bond's rise to the top of his game as 00 with M's downfall then maybe I could stomache it. But it won't be.
How would you suggest writing M's downfall into the film without it affecting Bond? If M is going down, Bond's fate is inexorably tied to her, since she is the one who found him, and he has so far managed to:
- Get caught on camera killing Mollaka after invading an embassy.
- Break into M's apartment and reveal that he knows her name (which is a closely-guarded secret).
- Miss Vesper Lynd's betrayal and lose $115 million in poker winnings in the process.
- Delivered Le Chiffre's body to the Americans, rather than take him alive.
- Failed to detain Craig Mitchell.
- Ignored a direct order to report in after the death of a Special Branch agent.
- Embarrass M by continuing to ignore orders to the point where the Foreign Secretary told her to bring him in.
Now, to be fair, a lot of these incidents have actually had positive effects. For example, when Bond killed Mollaka, it was because he knew Mollaka would report to his employer if he survived. Bond also found evidence that led him straight to that employer, and forced them to act knowing that he was prowling around. But when you look at it on paper, from a purely political standpoint - and M's downfall is likely to be politically-motivated - then Bond is a liability when all he has really been doing is making the best decision available based on whatever information he had at the time. A lot of the politicians wouldn't really be able to make that distinction; they'll just look back on it with 20/20 hindsight. M's comments to Villiers in CASINO ROYALE make it pretty clear that despite all their posturing, the politicians have no grasp of the situation (and that while she would privately give Bond a roasting, in public she was willing to back him if he could convince her to). So when those same politicians come looking for blood, they'll want to take down M and anyone connected to her.
You also point to M's micromanagement of Bond as a problem - why can't this be used in the film to fuel her downfall? She's not a particularly effective leader in that respect, and she's the head of a clandestine organisation. I can't imagine that it would sit too well with Downing Street that M cannot see the forest for the trees.