You may try with a replacement rule for display purposes only:

Quantity[3, "Kilonewtons" "Meters"] /.
 Quantity[n_, "Kilonewtons" "Meters"] :> Row[{n, "kN"*"m"}]

kN m or m kN is in fact the unit kJ or kiloJoule. If you demand the answers in kJ, there is no problem, and you are always in normal unit notation.

This isn't much of an answer, just a small clarification. Quantity does, in fact, hold the units argument, including the order in which you supply units. You can see this if you use FullForm. The display is being created as a special little display object in the front end. It's a bit like evaluating Red and seeing the little square. The actual result of evaluating Red is RGBColor[1, 0, 0], but what you see is a display object. Of course, none of that is helpful, because you probably don't want to look at raw Quantity expressions either.

I'm assuming that Mathematica is displaying units in some canonical order, and maybe standard units precede derived units. I'm guessing that you probably can change this by "pulling back the covers" and providing your own formatting code to make the boxes that represent Quantitys as display "objects". I don't know how to do that, but I've seen others do similar things. If you don't get an answer here, you might post (or search first) at the stack exchange for Mathematica: https://mathematica.stackexchange.com .

Actually, I was mistaken. Quantity does reorder units. I'm talking about the raw expression, not the display boxes form, (we already agreed the display form does reorder). Not sure why I didn't notice this before, but as I look at it now, it's what I would expect, since an expression like "kN" "m" is really just a Times expression.

By the way, that doesn't really contradict with the statement that Quantity has the HoldRest attribute. HoldRest just means that the arguments will be passed to Quantity unevaluated, but that doesn't mean that Quantity can't do its own evaluation/manipulation. It's not immediately obvious to me why Quantity needs the HoldRest attribute, but whatever.

One more slight nit. The response from Wolfram said: "Quantity ... ordering system ... is strictly alphabetical." I think that's confusing, since it describes the raw expression, not the display form. Consider the following:

So, in the raw expression, units are alphabetized, but that's probably just a result of the behavior of Times. In the display object, m comes before kN, which does not seem alphabetized. So, the display object is deliberately imposing an ordering based on something other than simple alphabetic order. Not sure if this matters at all in terms of any plans Wolfram might have for affording presentation flexibility with regard to units, but there might have been a slight miscommunication.