We have both maven2 and maven3 in hudson - and a lot of different jobs. Sonar execution with org.codehaus.mojo:sonar-maven-plugin:1.0-beta2:sonar runs fine.
I have a profile maven3 in our corporate pom to set the sonar plugin version to org.codehaus.mojo:sonar-maven-plugin:2.0-beta2:sonar.
To achieve this I check "Dont use global triggers configuration" in maven3 jobs and add "-Pmaven3" "additional properties" to get the correct version through a section which controls the version by using the pluginManagement section - this is however not applied by the hudson sonar execution.

/var/lib/jenkins/tools/apache-maven-3/bin/mvn -f /var/lib/hudson/workspace/pays-longbuild/trunk/pom.xml -Dintegration-test=true -Ddbunit.skip=false -DVERSION=1.1-SNAPSHOT -Dmaven.repo.local=/var/lib/hudson/workspace/pays-longbuild/.repository -e -B sonar:sonar -Dsonar.jdbc.driver=com.mysql.jdbc.Driver -Dsonar.jdbc.url=jdbc:mysql://sonar.edb.com:3306/sonar?autoReconnect=true&useUnicode=true&characterEncoding=utf8 ******** ******** -Dsonar.host.url=http://sonar.edb.com:9000

Note the missing -Pmaven3 parameter