I looked into IntelliJ 13.x and I was able to create JUnit runtime configuration. You need to do the following.
In your META-INF/plugin.xml
add dependency on JUnit plugin, otherwise necessary JUnit plugin classes will not be available in your plugin class loader.
<depends optional="false">JUnit</depends>
Here's the sample code to create JUnit runtime configuration. Although it works, it is just a stub, you will have to populate all attributes.
import com.intellij.execution.RunManager;
import com.intellij.execution.impl.RunManagerImpl;
import com.intellij.execution.impl.RunnerAndConfigurationSettingsImpl;
import com.intellij.execution.junit.JUnitConfigurationType;
import com.intellij.openapi.project.Project;
...
RunManagerImpl runManager = (RunManagerImpl) RunManager.getInstance(project);
JUnitConfigurationType type = JUnitConfigurationType.getInstance();
RunnerAndConfigurationSettingsImpl runnerAndConfigurationSettings = (RunnerAndConfigurationSettingsImpl)runManager.createRunConfiguration("junit test run", type.getConfigurationFactories()[0]);
runManager.addConfiguration(runnerAndConfigurationSettings, false);
And here we go, JUnit run configuration.
