Current working draft of autonomous docking code shutdown sequence. Untested.

DockShutdown.cs

// OnOff code seems to be global
ITerminalAction GetOnOffAction(IMyTerminalBlock block, bool enable)
{
    ITerminalAction Action;
    if (enable)
    {
        Action = block.GetActionWithName("Toggle block On");
    }
    else
    {
        Action = block.GetActionWithName("Toggle block Off");
    }
    return Action;
}

// Set all by type
void SetBlockStateByType<T>(bool enable)
{
    var blocks = new List<IMyTerminalBlock>();
    GridTerminalSystem.GetBlocksOfType<T>(blocks);

    if(blocks.Count > 0)
    {
        ITerminalAction Action = GetOnOffAction(blocks[0], enable);

        foreach(IMyTerminalBlock target in blocks)
        {
            Action.Apply(target);
        }
    }
}

// We want a remote (or local) control block with enough access to do what we want
IMyShipController GetFlightControl()
{
    var blocks = new List<IMyTerminalBlock>();
    GridTerminalSystem.GetBlocksOfType<IMyShipController>(blocks);

    foreach (IMyShipController block in blocks)
    {
        if(block.ControlThrusters && block.HandBrake && block.DampenersOverride && block.ControlWheels)
        {
            return block;
        }
    }

    return null;
}

// Set the state
void SetDockedState(bool enable)
{
    IMyShipController remote = GetFlightControl();
    if(remote == null)
    {
        SetBlockStateByType<IMyThrust>(enable);
    }
    else
    {
        // When we get on and off as distinct actions we'll be golden,
        // until then toggle unless you store state somewhere.
        remote.GetActionWithName("Inertia dampeners On/Off").Apply(remote);
        remote.GetActionWithName("Control thrusters On/Off").Apply(remote);
    }

    // Kill the gyro (or gyro array)
    SetBlockStateByType<IMyGyro>(enable);

    // Depending on your vessel you may want to power down weapons...
    SetBlockStateByType<IMySmallGatlingGun>(enable);
    SetBlockStateByType<IMyLargeGatlingTurret>(enable);
    SetBlockStateByType<IMySmallMissileLauncher>(enable);
    SetBlockStateByType<IMySmallMissileLauncherReload>(enable);
    SetBlockStateByType<IMyLargeMissileTurret>(enable);
}