It's hard to imagine preventing it in the books, because from the outside looking in, the Ministry needed to be corrupt for certain things, plot-wise, to happen. In the books, the Minister/Ministry is often seen as "the power(s) that be." In OotP, the Minister/Ministry's failure to support Harry in his time of need just added so much to the whole background of his story. A fifteen-year-old scholboy stood his ground, not only against the most evil wizard of all time, but also against the entire Ministry and the powerful man behind it.

During Fudge's reign of terror, I really don't think anything could have been done to bring him down. Doing so would have required a lot more time/effort than both Harry and Dumbledore had. There were a number of others who would have fought to bring down the corruption (i.e. Arthur and several others), but I think it would have required many more people stepping forward than just the few that I would imagine willing to doing so.