You can wrap that plugin under separate build profile and just enable that profile on the build that you want
For example:
<project>
...
<profile>
<id>generate-exe</id>
<build>
<plugins>
<plugin>
<!_- your plugin configuration -->
</plugin>
...
</plugins>
</build>
</profile>
...
</project>
Now pass parameter while launching maven to specify profile
For example:
mvn clean install -Pgenerate-exe