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This might be an old thread but I haven't seen a direct answer. I solved it by defining a world plugin that exposes the WorldPtr (see Gazebo World Class Reference) in the Load function and disabling the Physics Engine in the on_update method:

void DisablePlugin::Load(gazebo::physics::WorldPtr ptr, sdf::ElementPtr sdf) {
    _world = ptr;
    _update_connection = gazebo::event::Events::ConnectWorldUpdateBegin(
            boost::bind(&DisablePlugin::on_update, this, _1));
} 
void DisablePlugin::on_update(const gazebo::common::UpdateInfo& /*info*/) {
    if (_world->GetEnablePhysicsEngine())
        _world->EnablePhysicsEngine(false);
}

You can then set the pose of a model for example by using the SetLinkWorldPose method.