1 in 1000 of measles cases cause encephalitis.
<1 in 1,000,000 of MMR vaccinations cause encephalitis.
The above leads to some fun math.
http://www.cdc.gov/measles/about/overview.html
"Worldwide, there are estimated to be 20 million cases and 164,000 deaths each year."
If there are 20 million measles cases, you could expect 20 thousand cases of measles encephalitis.
To get 20 thousand cases of MMR encephalitis, you would need to vaccinate over 20 billion people. We obviously don't have that many. Instead, if we vaccinated the 7.1 billion people on earth, we could expect 7100 cases of MMR encephalitis, followed by the extinction of measles, mumps, and rubella. After which we'd never need to use the MMR vaccine again.