Reasoning behind אותו ואת בנו

All of this confusion comes together from the same place.

We say everyday Hashem Elokenu, that Hashem is our Elokenu Hashem Echad and that we proclaim that, in this there is no duality.

The implication is that, from our perspective, we might make that mistake. To think that the divine beyond division (Hashem) is separate from the divine within creation (Elokenu), within the seeming division. 

Then within the divine itself, to recognize the deeper concept of unity as well, first that the divine is not a composite existence etc as the Rambam explains. Then, to go deeper according to the Zohar and even deeper according to the Bal shem Tov. Recognizing how everything is truly nullified on a number of levels.

Now, by the same token, we must also recognize that "Hashem hu ha'Elokim" also means the Hashem, meaning his attribute of mercy, IS the Elokim, his attribute of judgment. The Zohar calls this "to include the right side in the left side." It's a recognition that while divine judgment is beyond our understanding, we know and believe that he is the ultimate of goodness and kindness. That the bad is actually divine mercy. 

We are supposed to reach the point where, in the days of Moshiach we say, "odecha Hashem ki anafta bi," "I acknowledge and praise you Hashem for getting angry with me." Yishaya 12:1

This follows the description in Yishaya 11 of how Moshiach will be a judge, but not in the traditional sense. Rather, he will judge with his "sense of smell." Meaning he will be able to express true justice in the world. Unlike today where judges are failable and confined by human ability. Moshiach will be able to go beyond that.

In the medrash Tana debei Eliyahu, it lists through all the nations and the difficulties they have given us through the generations and asks, "is there no fair judge for what they did to us? We are promised that there is. 

So, you see, to the harsh realities of this world, it is our job as Jews, and especially, as Chassidim (who always accentuate the positive) to keep in mind the Torah perspective that the difficulties ARE divine mercy. This idea is so integral that we proclaim it as the most basic article of faith in Shma Yisrael.

So no "suffering" or fire and brimstone end of days as this contradicts the basis of our faith. "Darcheya darchei noam," the Torah's "ways are pleasant ways."

Indeed, no one said it was easy. But as we have suffered through national tragedies, the destruction of the temple, pogroms and the holocaust we have been given the challenge of staying strong in our faith in the face of (no one said we could make sense of it with human intellect).

Through out, when we have been slaughtered al kidush Hashem, to sanctify G-ds name, the last thing we always proclaim is "Shma Yisrael", that we hold on to our faith inspite.

Another point. While the verse, "I thank you Hashem that you became angry with me" typically refers to the time to come, we are told in the gemara that, even now, just as we bless on the good we bless on the bad. Perhaps you're familiar with this blessing, "baruch dayan emes" blessed is the true judge that we say when someone passes away. Notice that we evoke this concept of Hashem's true judgment, as described for Moshiach etc, like it will be in the time to come, but in judgment of the current happenings. We proclaim, regardless of our heartache and inability to understand, that Hashem does understand and is the true judge of things, beyond human reason. Thus we connect the mourners comfort with that of Tzion and Yerushalayim, since that is when we will truly reach a cognizance of this higher truth.