How it works now

When a neighbour block changes and the block is powered and it isn't triggered (powered:1b) it will set its state to triggered and schedule a block update. If it isn't powered and triggered then it will be set itself as not triggered.

boolean isPowered = worldIn.isBlockPowered(pos);
boolean triggeredState = ((Boolean)state.getValue(TRIGGERED_PROP)).booleanValue();

if (isPowered && !triggeredState)
{
    worldIn.setBlockState(pos, state.withProperty(TRIGGERED_PROP, Boolean.valueOf(true)), 4);
    worldIn.scheduleUpdate(pos, this, this.tickRate(worldIn));
}
else if (!isPowered && triggeredState)
{
    worldIn.setBlockState(pos, state.withProperty(TRIGGERED_PROP, Boolean.valueOf(false)), 4);
}

When the block update happens the command will execute:

public void updateTick(World worldIn, BlockPos pos, IBlockState state, Random rand)
{
    TileEntity blockTileEntity = worldIn.getTileEntity(pos);

    if (blockTileEntity instanceof TileEntityCommandBlock)
    {
        ((TileEntityCommandBlock)blockTileEntity).getCommandBlockLogic().trigger(worldIn);
        worldIn.updateComparatorOutputLevel(pos, this);
    }
}

"CommandBlockLogic.java":

public void trigger(World worldIn)
{
    MinecraftServer server = MinecraftServer.getServer();

    if (server.isCommandBlocksEnabled())
    {
        ICommandManager commandManager = server.getCommandManager();
        this.lastOutput = null;
        this.successCount = commandManager.executeCommand(this, this.commandStored);
    }
    else
    {
        this.successCount = 0;
    }
}

In 1.9 I'm guessing they've added an if-statement to the trigger function to check what kind of command block it is executing from and if the block is powered. Why can't they just add a ! there? Please explain.