The jury system is not intended as a substitute for the law, it's intended as a safeguard to protect from the subjectivity of judges. Juries, like all of the legal system, are still intended to be subordinate to the legislative branch's decisions in terms of what is and isn't wrong.
Jury nullification is a weird rule that goes against the constitutional framework, but is so rarely used, at least for any important matter, that it has never really received too much scrutiny.
A lot has been written about this. The jury system has many purposes, but I don't think protection against individual subjective or corrupt judges are among the most important. (If anything, judges are much more likely to be objective than jurors.)
Rather, juries are generally a mechanism to prevent overreach by the executive (primarily) but also other branches of government (including the legislative branch). Not necessarily by going directly against laws (though that could also happen), but for instance by identifying laws that contradict the principles of the constitution. (Or other "deeper" laws, for that matter.)
Jefferson wrote : "Another apprehension is that a majority cannot be induced to adopt the trial by jury; and I consider that as the only anchor, ever yet imagined by man, by which a government can be held to the principles of it’s constitution." [1]
Now, a liberal interpretation of this is that a jury has an independent power, possibly even a duty, to disregard laws they consider to be against the legal basis (constitution, legal traditions, etc) of a country, basically overruling the legislative in such cases.
In fact, this type of thinking is probably a big part of the reason why the SCOTUS will not and can not override many aspects of jury verdicts. Specifically, even the SCOTUS cannot overturn an aquittal.
In other cases (such as when the SCOTUS thinks the jury has violated the constitution, due process hasn't been followed, etc) it will instead invalidate a decision. (Which can lead to the case being dismissed or to a retrial, depending on the details)
Jury nullification is a weird rule that goes against the constitutional framework, but is so rarely used, at least for any important matter, that it has never really received too much scrutiny.