I'll use the provided translation, which should be good enough for the purpose of this argument.
Here's article 142 with emphasis added:
Article 142: If the Chancellor of Justice finds that legislation passed by the legislative or executive powers or by a local government is in conflict with the Constitution or a law, he or she shall propose to the body which passed the legislation to bring the legislation into conformity with the Constitution or the law within twenty days.
Where I'm getting at is this language suggests is that "the Constitution" isn't "the law", they are technically different. It could be a mistranslation or misinterpretation. However, I feel confident enough because that's a fairly common idea that constitutions and laws are different.
Examples of how laws are different from the Constitution include that laws can be initiated by "a member of the Riigikogu" (art 103) whereas constitutional amendements require "not less than one-fifth of the membership of the Riigikogu" or "the President of the Republic" (art 161). The Constitution cannot be amended during a "state of war", whereas no such restriction exist on laws.
So here's Article 12 again with emphasis added:
Article 12: Everyone is equal before the law. No one shall be discriminated against on the basis of nationality, race, color, sex, language, origin, religion, political or other opinion, property or social status, or on other grounds.
Note that it says "before the law", not "before the Constitution".
If we accept that the law and the Constitution are indeed different, and if we accept that article 12 puts a restriction on the law rather than the Constitution, then there is no contradiction.
If we don't accept that, then the Constitution taken as a whole still says "no discrimination, and also there is this one very specific and narrow case where discrimination is mandatory". You can view it as a contradiction, but it's better viewed as an exception.
What the Constitution says is by definition constitutional, so this one exception is constitutional. You can call it contradictory if you want, but at the end of the day it is what it is.
You could conceivably challenge the Constitution, and the process should be outlined in the Constitution or a document referenced in the Constitution. As far as I can tell, it involves bringing a case to the Riigikohus, the Supreme Court of Estonia, and ultimately that's where interpretation of the Constitution rests.
If no one has successfully challenged it and it's in the Constitution, chances are nobody objects to the common interpretation that article 57 is a slight and justified exception to article 12.