Perhaps you misunderstood me. If Congress were to pass a statute which would contradict the Constitution, judges would be duty-bound to regard it as void. The statute would not be void because the judges declared it to be so; it would be void because the Supreme Law of the Land declared it to be so. Conversely, if Congress passes a legitimate statute, judges are duty-bound to uphold it, since the Constitution specifies that legitimate statutes are part of the Supreme Law of the Land.
The difficulty comes not from recognizing that judges are duty-bound to regard illegitimate statutes as void and legitimate statutes is valid, but rather from an unwillingness to recognizes that not all judicial decisions are legitimate. It is that unwillingness to question the legitimacy of judicial decisions that has enabled the gross judicial overstepping of authority.
Further, while courts have, and require, legitimate authority to draft and apply interim rules when necessary to resolve ambiguities in existing laws, this does not grant such interim rules any authority beyond what's necessary to resolve ambiguity. Only in cases where ambiguity can be demonstrated without regard to precedent should precedent even be considered. Otherwise, if existing rules would be unambiguous, precedent is either going to be (1) inapplicable to the present situation, because something in the case is different; (2) redundant, since the outcome it would compel would have been reached even in its absence; or (3) illegitimate, because it was decided contrary to what the law requires.
While a federal statute may legitimately restrict a class of actions which would typically affect interstate commerce in various ways without stating a specific nexus (since different actions in the class might affect interstate commerce in different ways), a prosecutor bringing charges under such a statute should be required to convince a jury that allowing the defendant's particular actions would interfere with the government's authority to regulate interstate commerce. Likewise, prosecutors should be required not only to convince a judge that evidence was not gathered in patently-illegitimate fashion, but also convince a jury that things like searches were "reasonable", that bona fide "probable cause" existed, etc. Note that in many cases, such determinations will depend on things like witness credibility, which are clearly matters for jurors rather than judges to determine.
The importance of jurors, however, does not imply that resolutions of ambiguous laws should never fall to judges. Among other things, of neither party in a case requests a jury trial, the matter will quite legitimately fall to a trial judge for determination. At some point, a judge will have to render a decision in a case where the law is truly ambiguous. And in such a case, the judge is the person with the authority to resolve such ambiguity.