Vito was smart enough to change with the times. As his reach become longer - beyond one neighborhood - he needed to use the "legitimate" system to reinforce his power. Certainly, he couldn't bribe the entire law enforcement/judicial system, so he worked within the system as well as outside of it.

The Corleones used whatever means were most apt to achieve their goals. In the scene outside the hospital, they were outmanned and outgunned. Tom, realizing this, uses the threat of judicial review of McCluskey's actions to ensure that Vito was protected. No amount of buttonmen would have accomplished that.