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When the Rebels decided to fight back against the Inquisitors and sought Yoda's advice for help, Yoda told them to go to Malachor.
Why there of all places? Surely not so they could employ the Sith superweapon located there? Or is it a test? Or did he have visions of the events that could ensue if he sent them there?
Why exactly did he send them to a world forbidden to the Jedi Order since long before the days of the Galactic Republic?
Because Ezra and the others had chosen to fight and the information in the holocron on Malachor would help them.
Here is the summary of the exchange between Ezra and Yoda (emphasis mine).
Ezra asks Yoda if the Jedi Master has the power to destroy Vader and the Inquisitors. Yoda tells him that there were once thousands of Jedi, before they chose to join the Clone Wars. Yoda explained that, in the Order's arrogance, they joined the conflict too quickly. Fear, anger, and hate gripped the Jedi Order, and the Jedi were consumed by the dark side.
Ezra asks if it was wrong for the Jedi to fight or if it is wrong for him to protect his friends. Yoda says that he too fought for many years, because he was consumed by fear. Ezra is surprised that Yoda was once consumed by fear, but Yoda explains that it is a lifelong challenge to avoid bending fear into anger.
Suddenly, the chamber begins to shake, and Yoda says that the enemy has found them. Ezra, however, is not yet willing to leave, and asks Yoda how the rebels are supposed to win if they do not fight back. Yoda says the real question is how the Jedi choose to win, and Ezra says they have already chosen to fight. Reluctantly, Yoda tells Ezra to find Malachor and then disappears.
Star Wars Rebels: Shroud of Darkness
So it is clear Yoda thinks there is a better path, but since Ezra and the others have made up their minds, he gives them the hint needed to get more information (go to Malachor) to make them more effective in their fight.
Ezra is skirting close to Dark Side. He wants to destroy (i.e. kill) Vader and Inquisitors. He has chosen to fight. Of course, this is not unusual, Yoda has seen this in Padawans many times. What is different is Yoda's response. Yoda is wiser now. He knows from his own experience that everybody, including him, has Dark Side inside. No longer he tries to falsely shield Padawans from themselves.
Yoda lets Force guide Ezra. On Malachor, Ezra could find what he seeks, one way or another. He could witness destructiveness of conflict that consumed both Jedi and Sith. Or he could join Maul. Maul is certainly capable of destroying Inquisitors, and if he trained Ezra, who knows ... maybe two of them could defeat Vader. After all, Ezra and Kanan almost did that once with their combined powers. So, there is a path of wisdom and a path of sword for Ezra. Yoda moves away from traditional Jedi training, and lets Living Force do it's thing (influence of Qui-Gon Jinn)
Malachor is also Trial of Flesh for Kanan Jarrus. Kanan lost his physical sight in order to get deeper insight into the Force. He also lost part of his previous self - he now wears Jedi Temple Guards mask, and in this way he loses his old identity in order to become guardian of the Order and Ezra himself. In a sense, he now goes full circle in replacing former Temple Guard - Grand Inquisitor. His greatest, now dead opponent, but also person who knighted him in his vision. Jarrus becomes what Grand Inquisitor failed to be .
Malachor is also trial of destiny for Ahsoka. Ahsoka simply cannot let past be past. She is attached to her former master, determined not to abandon him this time . She subconsciously blames herself for what has happened to him, and that determines her fate.
P.S. Of course, out of universe, Malachor is convenient place for grand Season finale, place not connected with main story of Rebellion in any way, with powerful but ultimately impotent Sith temple-weapon that also does not change main storyline . Additional bonus for introduction of Maul and elimination of Ahsoka (at least for Season 3). Such place is naturally only known to very wise, therefore vision of Yoda .
