You need to be perfectly aware of the consequences of what you want to do: the effective POM will also contain your current settings (content of settings.xml), thereby possibly publicly exposing whatever passwords you have hard-coded in there. A better solution would be just to deploy the parent POM.
However, if you really want to go down that path, you can have the following configuration:
<plugin>
    <artifactId>maven-jar-plugin</artifactId>
    <version>2.4</version>
    <configuration>
        <archive>
            <addMavenDescriptor>false</addMavenDescriptor>
        </archive>
    </configuration>
</plugin>
<plugin>
    <artifactId>maven-help-plugin</artifactId>
    <version>2.1.1</version>
    <executions>
        <execution>
            <phase>generate-resources</phase>
            <goals>
                <goal>effective-pom</goal>
            </goals>
            <configuration>
                <output>${project.build.outputDirectory}/META-INF/maven/${project.groupId}/${project.artifactId}/pom.xml</output>
            </configuration>
        </execution>
    </executions>
</plugin>
This tells the maven-jar-plugin not to add the Maven descriptor pom.xml and pom.properties to the jar. Instead, the pom.xml is generated by the maven-help-plugin and its effective-pom goal.
If you want the pom.properties file also, you will need to create it manually with the maven-antrun-plugin.