So you're looking for a field of large-scale system design and hoping that the insights of such a discipline will avert shortsighted government decisions that don't account for the larger context (whatever that context may be). I've been looking for the same thing, just from the other direction. I don't claim to have an answer, but I can claim some professional experience in the area.
To unpack the jargon, system engineering is the discipline of engineering entire systems, as opposed to engineering a stand-alone widget or a stand-alone computer. A related discipline is decision analysis, which is the field I work in.
If systems engineering is the discipline that tackles your first desire (a discipline of large-scale system design), decision analysis is the discipline that deals with your second desire (avert government decisions that don't view a problem in the context of everything else--to borrow Thomas Barnett's favorite phrase). It seeks to improve decision-making by bringing analytic approaches to bear. To be clear, the goal is not to replace the human decision-maker; it is rather to challenge, refine and improve human intuition.
I spend my days worrying about how to distill the tradeoffs a sponsor faces, so that they can better understand the consequences of this or that choice. I build mathematical models, use optimization tools, and try to get inside the head of the decision maker. (That last task is by far the hardest.)
The cutting edge of system engineering is in fields like complex system design, engineering large systems--basically pushing the upper threshold of the discipline. The question driving these fields is: How can we understand and manage huge and complicated systems?
While we recognize that there are theoretical limits to analytic methods (game theory, decision analysis, RAND's 1950s dream of a "science of strategy") in problem-solving, we are nowhere close to implementing even the most elementary of these approaches.
Most of the successes I've seen, when it comes to applying this stuff, comes from using the most elementary of analytic approaches. The scale of complexity that we can handle is expanding and there are great methods for improving decision-making just waiting to be used. And we need it all so badly.
Despite all this work, I still feel that we are winging it when it comes to joining the technical study of systems with the practical job of changing how the government deals with the world.
Plenty of decision analysts aren't at all concerned with the problems the government faces. Similarly, plenty of public policy/ political science/ international relations wonks aren't at all concerned with trying to truly understand the governing dynamics of the systems of the world.
(Had there been more of that sort of thinking in the fields I might have stuck with political science or international relations instead of ending up a math major.)
A year or two ago I thought that such a field existed--this mystical blend of analytic and qualitative thinking about the problems of government. I've come to realize there isn't any discipline that neatly encompasses it. But there are tantalizing pieces floating about.
[Signed] Manila in USA"
For a historian's take on the Stuck at the intersection... essays, see Mark Safranski's To think strategically you must think systematically.
For a look at an organized attempt to apply systems thinking to a range of activities, including public policy/planning, visit the Systems Dynamics Society for links to papers by Jay W. Forrester, who developed a methodology for studying and managing complex feedback systems.