My team works around this problem by wrapping the relevant configuration in a profile:
<profile>
<id>only-eclipse</id>
<activation>
<property>
<name>m2e.version</name>
</property>
</activation>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
...
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
</profile>