Jake - I don't really see what your proposed reorganisation would add to anything.
For one thing, it assumes (as does the existing infrastructure, but to a far lesser degree) a fairly clear-cut distinction between threats abroad and threats at home. Seems reasonable, but this is something that security forces have long had trouble putting into practice. The available records we have of MI5 or MI6's operations during WW2, for instance, indicate frequent overlapping of remits and infighting that derived from this.
Furthermore, assuming that something is less dangerous because it is far away really isn't a valid assumption in the modern world. Regardless of whether you agree with the campaign in Afghanistan or not (and most people seem not to), it does largely seem to have been motivated by a response to 9/11 and a desire to attack those responsible. Foreign and domestic threats are often interconnected and based on what limited evidence we have, dividing the response to them too deeply doesn't seem to have a particularly good track record.