But what reason can they point to for saying that "We should not regard this as good"?
In short, their own internal value-judgements and estimations. Since what actually acquires the "Good"-mana is open to opinion anyway, their judgements are as worthy as the consensus. The more they get people to think like them, the more the consensus shifts to model their version of what their ideal world is, the more the planes rearrange themselves to be what they believe they should be.
Should is a verb that is begging for reasons. But what reasons can the person in Planescape bring to bear, given that the evaluative vocabulary that would normally be used to provide the reasons has already had its reference determined by consensus?
The reasons are particular and individual. The consensus is formed out of uncountable multitudes of particular and individual beliefs. As a PS character, you likely have reason to dispute this consensus that is particular and individual, and seek to change the beliefs of those uncountable multitudes to match your own.
For instance, a child on the streets of Sigil might grow up in the shadow of a serial murderer whose damaged mind results in a crime spree that terrifies this child's neighborhood. The murderer is eventually killed in the street by a band of enforcers. This seminal moment in the child's life becomes something they return to, to try and understand over and over again - why did this happen? How can it be prevented? You learn of the Harmonium and their efforts to correct the thoughts of damaged minds, to rehabilitate the mentally defective into functioning members of society. You understand that this would have prevented that serial murderer from terrifying the neighborhood, if he was just noticed early enough and given this treatment. Not only this murderer, but others, in the future, may be prevented by this. You join the Harmonium to advance this work, which you see as something unquestionably worthy of Good-mana, an act of compassion and a protection of innocents not unlike what the Archons and Guardinals are known for. So it surprises you to learn that the consensus disagrees - that this program has caused a layer of Arcadia to lose that Good-mana, because of the consensus that robbing someone of free will is not worthy of that Good-mana.
Thus, you set out to change that opinion, so that your view becomes the consensus. You fight demon cults who delight in madness. You convince reluctant eladrin who see this as eroding individual conscience that this is for when that conscience goes awry. You weed out the devils and the power-mad seeking to use the mind control for selfish ends from your own organization. Guardinals begin taking up the same techniques. Slowly, the view of coercive mind control begins to match what you believe it should be - as a tool for the betterment of all. Consensus shifts, the layer is restored to Arcadia (heck, maybe Celestia gains a few new layers!), angels being to use your tools to heal the mentally ill, fewer children suffer your childhood fate of being terrorized by madness, social order increases, and you are shown to be correct (because people believe you to be so).
Your reason for believing this is your own reason, personal to you. Because the consensus forms the idea of what is Good-aligned and what isn't, your desire to change that consensus needs no reasoning beyond your personal push. Much as happens in the real world, individuals decide for themselves, based on their culture, context, and experiences, what the world they're in should look like. In PS, as a PC, you then go out and shape the world to be that.