I'm with Eric; wherever possible use an existing mechanism rather than add a new one. Attacks on flank and rear means the unit fights with half dice, as if Pinned. And then the rule lawyers will want to discuss from where the attacker has to start its move in order to count as being on the flank or rear...
You risk over-complicating a very good rule set if you start adding too many modifiers like 'secure flanks and rear' or adding Skirmish order as a third formation. Having said that, there are tweaks worth considering, some generic and others period-specific for added period feel.
For larger games, we've also restricted Volley Fire to targets directly to the front of the firers.
Units testing to rally at 50% strength or less do so at a further -1 modifier, and units at 25% or less that fail any Rally test are automatically removed whatever the final score (not just 2 or less) - this removes all those irritating 2-3 figure units that refuse to go away and clutter up the table.
In our Zulu games so far we've ruled that British regular infantry and cavalry do not have to take a Pinning test in response to the destruction/removal of a friendly native unit.
We use Force Leaders (1 per 24 points) for larger games where we don't want to have individual unit leader traits. They have Move as a Free Action, usually as Cavalry of an appropriate type. They have their own Leadership value and trait as usual. They give a +1 modifier to Rally tests made by any unit within 6" unless their trait suggests otherwise (Hapless, Brutal, Shirker etc). They can also join a unit and assume command, using their Leadership instead of that of the unit (usually useful if the unit is Leaderless or led by a Hapless type). Traits only apply to the Leader himself and any unit he is attached to. An unattached Leader may not be fired on but may be Attacked, fighting with 2 dice. A Leader is never Pinned but leaving a Pinned Unit means a further -1 modifier when that unit next tests to Rally and it cannot count the effect of the Leader being within 6".
I think MWWBK gives us a great too-kit with which to construct our own set of 'perfect' colonial rules based on our own preconceptions, much as Dan himself says in the section on optional rules.
One final point; is it me, or is the layout of the rulebook really confusing? I find myself constantly flicking through trying to find the relevant section I need. It's got a lot better since I put together my own QR sheet, which I'm using with unit reference cards similar to those designed by Mr Shed.