A goal can be bound to a phase by specifying a new execution for the plugin. I'm assuming you've got some custom stuff you need to make most of this work correctly, so I'm just going to focus on what should work to bind a plugin goal to a particular phase.
<plugin>
<artifactId>gwt-maven-plugin</artifactId>
...
<executions>
<execution>
<id>gwt-site</id>
<phase>site</phase><!-- phase to bind to -->
<goals>
<goal>compile</goal><!-- goal to run in that phase -->
</goals>
<configuration>
<!-- Your magic configuration stuff goes here -->
</configuration>
</execution>
<!-- Possible other executions might be defined here -->
</executions>
</plugin>
Preventing the default maven site from being run is more interesting, as it is a phase, with a variety of goals bound to it. The standard site:site goal can be prevented from running in the site phase by explicitly specifying an execution with no goals. This may vary slightly from maven 2 to 3, so I'm going to be a little general here. Take a look at your build logs to see what is currently specified in terms of execution id, group/artifact id to correct possible oversights in my example:
<plugin>
<artifactId>maven-site-plugin</artifactId>
...
<executions>
<execution>
<phase>site</phase>
<goals></goals><!-- This is empty to indicate that no goals should be run in this phase -->
</execution>
</executions>
</plugin>