what does "If toes were stepped on"mean?
Yung-cheng believed that the empire needed a house cleaning and so relied upon the kind of officials who were not afraid to punish underlings or impeach superiors. If toes were stepped on, that was all the more evidence of genuine administrative reforms. For, more than anv other Manchu emperor, Yung-cheng was re¬solved to rationalize the fiscal policies and bureaucratic institutions that had been copied from the late Ming period.

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If you step on someone's toes it means that you offend or insult that person.

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I would like to add that "to step on toes" or "someone's toes were stepped on" is not used for all types of offense or insults.  For example, if Person A calls Person B an idiot, he has offended and insulted Person B, but he has not stepped on Person B's toes.  Instead, "to step on someone's toes" or "someone's toes were stepped on" is used in situations where a person involves himself in a situation which is really someone else's responsibility, and the other person becomes upset or feels insulted that someone interfered in his business.

In your post, Yueng-cheng relied on certain officials who took certain actions which may have been the responsibiity of other government officials, and the other officials may have felt offended or insulted.