The plugin is not deprecated, only the sonar-maven job type. There are several ways of running an analysis with the plugin.
We
feel that it is better to use Jenkins' standard maven target (in a
Freestyle project or maven project) with the new functionality of
injecting the sonarqube configuration as environment variables.
This ensures that you do not rely on our adaptation of the maven job, and instead use the standard one.
You can find the documentation, with an example here:
http://docs.sonarqube.org/display/PLUG/Triggering+SonarQube+analysis+on+a+Jenkins+JobAs
you can see in the doc, there is no need to change anything in the
projects, not even in the SonarQube configuration in Jenkins.
In any case, we do not plan to remove the sonar maven job type anytime soon.
BR