Leverage compels the innocent to plead guilty, and the thought exercise of "crashing the system" will not work because the stakes are too high. There's usually evidence such that a refusal to plead guilty will not affect the outcome very much. Applied to purely innocent suspects, there is no guarantee that refusing to plead will result in a not guilty verdict.
The same sort of problem is present in the investment markets. The fact that something might be over-leveraged as the fundamentals deteriorate does not guarantee profits if you try to short. To quote Keynes, (possibly the one thing he wrote that I whole-heartedly agree with) "Markets can remain irrational far longer than you or I can remain solvent."
It's quite possible that overworked juries and judges would wrongly convict more people by rushing to judgment if they had 10 times the caseload.
Crashing the over-leveraged legal system by flooding it with not guilty pleas may not cause the system to blink; instead, it might cause the courts to degenerate into a Kafkaesque nightmare.
I think this article's gist is that the American judiciary is leveraged and thus vulnerable to disruption. The solution advocated, loosening laws to decrease case volume, is probably better than the alternative of directing more funding to the courts and prison system.
This systemic leverage pushes the judiciary to do unsavoury things, such as courts increasing penalties for those who choose trial by jury and over-zealous AGs putting elections above fairness.
It may be hyperbole to call shining light on potential civil liberty abuses petty.
>people tend to support the system
As of 2011 the US judiciary stood at 63% approval [1] - this is a good, especially when compared to Congressional approval, but the lowest since 1973. People also tend to pay less attention to the judicial than executive and legislative branches.
[1] http://www.gallup.com/poll/149906/supreme-court-approval-rat...