Amnesty law Found Unconstitutional in Uruguay: Victory for Human Rights, but what about popular sovereignty?

On monday, the Supreme Court of Uruguay issued a decision condemning the 1986 amnesty law for crimes commited under the military regime that was in power until 1985. I'm not familiar with the constitutional framework in Uruguay and the legal consequences of the decisions. Some report that the law was declared "unconstitutional" (see here): does it mean that the law is immediately inapplicable? Others report that the law was "annuled" (see here). I haven't read the decision (if someone has it in English, i'd appreciate receiving it!) but apparently, the Court invoked Uruguay's human rights obligations to respect victim's right to reparations and to know the truth.

This is a new decision in the trend against amnisties in international law, and is, in this sense not particularly groudbreaking. I won't go into a debate here on the general question of Amnisties (I invite you to read my forthcoming paper on this). What strikes me more particularly in this case, beyond the legal technicalities, is that the law was upheld by referendum, not once, but twice, the last time as recently as 2009, despite strong opposition from rights groups. I find it a little disturbing, in the broader political scheme of things, that the democratic popular expression of opinion be given so little consideration. In 2009, after the referendum, the regional director of HRW said that: "let's not forget that  accountability is not a popular contest that should be decided by majorities". Actually, it kind of is. Society makes a choice to criminalize some conducts and not others. And the least worst way we have come up to evaluate support for such choices is requiring a majority. In other words democracy. What kind of arbitrary criteria allows HRW to decree that democracy is a good thing, except when people don't vote "right"? If the referendum had gone the other way, I'm sure that same person would have applauded the popular support against amnisties.

It is a difficult balance to be struck between majority decisions and minority opinions in any democracy, and a harder balance even between human rights and political compromise in situations of transitions, and I  certainly do not claim to have the answer. But as a rule, I would tend to give quite some credit to the free expression of public opinion as a starting point. The majority principle (with qualifiers or not), is effective in that it allows institutions to move forward. Whereas, minority power can only lead to political stalemate. This is of course schematic, and doesn't mean that there shouldn't be any normative framework (both procedural and substantial) surrounding the exercice of democratic expression. But as a rule of thumb, I have difficulty seeing how a law disapproved by a majority can be politically legitimate.

This reasoning of course implies adopting a collective/social contract approach to political analysis, which is a little removed from the individual approach, where rights emerge from above and social relationships are totally depoliticised. Indeed, how could they not be where the origin of rights is transcendental, rather than emerging from some form of popular consensus? you cannot argue with a priori morality. I find it ironic that such effort was put by intellectual and political leaders over the centuries to free themselves from the Church by breaking down the conflation between the temporal power and the spiritual power, only to see the latter re-enter through the prism of Universal Human Rights in recent years. Apparently, nothing much has changed since the Middle Ages...