Concidering Anarchy

That's your reading? It certainly isn't mine, since the Harmonium was consistently portrayed as errant blowhard who made a huge mistake (and lost and entire planar layer) and the Mercykillers got ganked way harder than any other faction during the Faction War.

The Faction with the most real evidence for favoritism is the Ciphers, a faction with no enemies that got a complete pass on faction war and who faction weakness was written totally without mechanics (making it easy for creative players to dodge, and difficult for DMs to deal with without brutally curtailing the random insanity that makes gaming around a table so much fun).

I would add that in makes a great deal of practical sense to portray the Revolutionary League in a poor light because as they were initially written up they were unplayable in most gaming groups because they required one member of the party to hold an agenda different from the rest and hide behind a mask. This goes totally counter to the 'band of heroes' nature of D&D where even evil parties tend to work with a relatively high degree of cohesion (this doesn't have to be the case of course, but D&D was not designed to handle party backstabbing and in-fighting, an is vastly inferior to something like Vampire for handling that type of experience).

As for the internal distrust issue, it is very important to remember that unlike real-world anti-establishment groups, the Revolutionary league is opposed to effectively all aspects of the existing order. They don't have any sort of semi-unified vision of what the world would look like when their cause is accomplished, and as a result are extremely suspicious of other cells of their faction attempting to impose a kind of order they disagree with upon the multiverse, or for the even more likely threat of corruption in the ranks. Individual Revolutionary League 'cells' may have a good deal of internal unity, but the faction as a whole represents a vast kaleidoscope of differing visions that will conflict more often than not (real-world revolutionary groups conflict all the time).

Alisohn Nilesia, the Mercykiller factol, is also 100% insane. She thinks that her ultimate goal in life is to find what the Lady of Pain is guilty of and punish her for it, and instituted sentencing "reforms" the entirety of which are comprised of "10 years for misdemeanors, death for felonies". There's also a strong hinting (even outright admitted in the Manifesto in certain specific cases) that Nilesia assassinated basically everyone that would be in her way of becoming factol, including her own foster mother, the former factol, and an entire swath of Mercykiller veterans that were unsure about her ascent

As for the faction itself, Arwyl Swan's Son is certainly characterized as you've described the faction as are his followers, but he's just one force. There's a huge group within the faction that is completely opposed to even the concept of extenuating circumstances, of which Nilesia is the biggest example. The division between the Sons of Mercy and the Sodkillers was still existent to some degree even before Faction War, if unofficially, and they certainly weren't all the paragon of moral role models that you've characterized them as.

I'm not sure why you think the anarchists are opposed only to the Harmonium, nor do I understand the critique that you think the anarchists have no goals other than disestablishment.

In the first case, it is made pretty clear that the Anarchists have cells in every faction. At one point, they even assassinated many of the faction heads within a short space of time. Their unifying goal is to overthrow the existing establishment. Naturally, as is the nature of revolutionary groups, not everyone agrees about what to do afterwords. The fact that they don't necessarily all agree doesn't mean they don't still have other goals. The point is, their central theme is to topple established authority because of a central belief that authority and power is corrupting and abusive. Naturally they are more opposed to factions like the Harmonium, simply because the Harmonium is the faction that polices Sigil. It follows that they would therefore be the faction that has the most interest in actively interfering with the Anarchists, and vice versa.

I think part of your discomfort with the Planescape portrayal of Anarchists seems to be based on the fact that you have a distinctly modern view of the anarchist movement. Modern anarchism, while still generally agreeing on the disestablishment line, has evolved into a sort of catch all for militant activism. Some guys have developed particular philosophies of anarchism such as John Zirzan and his primitivist views. Others are generally pro-environment. Others are more into ideas of "self organizing societies" and so forth.

The thing is, these modern anarchists have little in common with the roots of anarchism as a movement in the 19th century. 19th century anarchism is very much like the anarchism portrayed in Planescape. They were terribly violent, extremely paranoid (with good reason), frequently engaged in assassination, had no real unified vision or power struggle, and really were only unified in so far as they used any means necessary to overthrow existing governments. When it came to the details of the "aftermath" their wasn't the slightest bit of coherence between one group or the next, or than perhaps some vague "progressive" vision (a vision that often as not would probably be laughed at by modern day anarchists). This anarchism was largely a response to the rapid changes brought on but industrialism, the vast gulf growing between rich and poor and specific political grievances usually in repressive tyrannical governments. Sometimes it was a rebellion against all three such as Czarist Russia or Hapsburg Austro-Hungary. There was an existential crisis in Europe brought on by the industrial revolution, and some people turned to Anarchism as a way to fight those changes.

In these anarchist cells, intragroup murder wasn't that infrequent, the risk of capture by authorities was great, and the consequences of such capture was almost certain death. The stakes were high, and the abuses being fought against were an in-your-face kind of inhumanity. The anarchists of that time have little in common with the much more pacified anarchists of today. Similarly the abuses of today just don't have the same visceral impact of the conditions of the 19th century. You may argue that the issues are more important today, but the fact is the suffering in, say, 19th century Russia was something that was human in nature, was readily apparent to everyone, was present nearly all the time, and was on such a massive scale that it wasn't really a matter of debate and uncertainty as with modern issues so much as it was an issue of who held the power and who should pay.

A good novel on the issue, albeit one slanted against the anarchists is Dostoevsky's The Devils (or The Demons depending upon the translation). This is particularly insightful if you read The Notes From the underground first, written when Dostoevsky actually was in an anarchist circle. The views you get there are just worlds apart from modern anarchists. I sort of consider those two books to be a great source of inspiration for how to run anarchists in Planescape.