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I'm not sure what your problem is exactly, but here's what I do to get a current version of gazebo running with ros groovy:

We are running the the catkin_groovy gazebo version (branch):

sudo -E apt-get install build-essential libtinyxml-dev libtbb-dev libxml2-dev libqt4-dev pkg-config libprotoc-dev libfreeimage-dev libprotobuf-dev protobuf-compiler libboost-all-dev freeglut3-dev cmake libogre-dev libtar-dev libcurl4-openssl-dev libcegui-mk2-dev mercurial checkinstall git-core
cd
hg clone https://bitbucket.org/osrf/gazebo ~/gazebo -b catkin_groovy
mkdir ~/gazebo/build && cd ~/gazebo/build
source /opt/ros/groovy/setup.bash
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local
make # this takes some time ... to boost use -jx
sudo checkinstall -y --pkgname=Gazebo --pkgversion=1.X-YYYY # where X is the gazebo version and YYYY is the repository version, preferred over make install since it can be removed easily
sudo ldconfig

I'm not sure what your problem is is, exactly, but maybe you want to exchange the controller tag with a plugin tag such as:

<gazebo reference="link_joint">
  <plugin name="gazebo_ros_force" plugin="libgazebo_ros_force.so">
    <alwaysOn>true</alwaysOn>
    <update>100</update>
    <updateRate>100.0</updateRate>
    <bodyName>link</bodyName>
    <topicName>force</topicName>
  </plugin>
</gazebo>

And here's what I do to get a current version of gazebo running with ros groovy:

We are running the the catkin_groovy gazebo version (branch):

sudo -E apt-get install build-essential libtinyxml-dev libtbb-dev libxml2-dev libqt4-dev pkg-config libprotoc-dev libfreeimage-dev libprotobuf-dev protobuf-compiler libboost-all-dev freeglut3-dev cmake libogre-dev libtar-dev libcurl4-openssl-dev libcegui-mk2-dev mercurial checkinstall git-core
cd
hg clone https://bitbucket.org/osrf/gazebo ~/gazebo -b catkin_groovy
mkdir ~/gazebo/build && cd ~/gazebo/build
source /opt/ros/groovy/setup.bash
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local
make # this takes some time ... to boost use -jx
sudo checkinstall -y --pkgname=Gazebo --pkgversion=1.X-YYYY # where X is the gazebo version and YYYY is the repository version, preferred over make install since it can be removed easily
sudo ldconfig

I'm not sure what your problem is, exactly, maybe you want to exchange the controller <controller> tag with a plugin tag such as:

<gazebo reference="link_joint">
  <plugin name="gazebo_ros_force" plugin="libgazebo_ros_force.so">
    <alwaysOn>true</alwaysOn>
    <update>100</update>
    <updateRate>100.0</updateRate>
    <bodyName>link</bodyName>
    <topicName>force</topicName>
  </plugin>
</gazebo>

And here's what I do to get a current version of gazebo running with ros groovy:

We are running the the catkin_groovy gazebo version (branch):

sudo -E apt-get install build-essential libtinyxml-dev libtbb-dev libxml2-dev libqt4-dev pkg-config libprotoc-dev libfreeimage-dev libprotobuf-dev protobuf-compiler libboost-all-dev freeglut3-dev cmake libogre-dev libtar-dev libcurl4-openssl-dev libcegui-mk2-dev mercurial checkinstall git-core
cd
hg clone https://bitbucket.org/osrf/gazebo ~/gazebo -b catkin_groovy
mkdir ~/gazebo/build && cd ~/gazebo/build
source /opt/ros/groovy/setup.bash
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local
make # this takes some time ... to boost use -jx
sudo checkinstall -y --pkgname=Gazebo --pkgversion=1.X-YYYY # where X is the gazebo version and YYYY is the repository version, preferred over make install since it can be removed easily
sudo ldconfig