...because he didn´t go to Berlin.
The story of such a demontage in an one-party state like Bavaria with the CSU  is very interesting for the aficionados of politics.
You are right, the polls with the CSU under 50% are prrobably the argument for the putschists.
But in my opinion the trigger was the hesitation-Walz of stoiber between Berlin and Munich after the last national elections, he retreated from the notional challenge for going back to the more secure post of Bavaria Ministerpräsident.  That plus his not leading anything about the health reform, he lost his status of leader in the minds of the bavarian and of his party underlings. The emperor had no clothes .
Thus at least in part the sinking polls and the late revolt.
Like a pack wolf sniffing a weakness.

A funny anecdote: some anonymous opponents internal painted on a bridge over his daily road to home "goodbye Edi" some days before the decisive battle.

It worked. Worth repeating in other countries? ;-)

La répartie est dans l'escalier. Elle revient de suite.