This is an interesting topic and I have taken to liberty of excerpting from a paper I wrote a couple of years ago on rebels in Japan. In a society as hierarchical as Japan the idea of the 'rebel' is not as widely romanticized as it is in the individualistic West, in part due to Chinese Confucian influence on East Asian society generally, but also due to indigenous Japanese feudal and political ideals. The Shinsengumi occupy a unique position in the modern Japanese 'honourable rebel' paradigm.

Even more than the Second World War and it’s decisive conclusion, the Meiji Restoration and the Boshin War (1868-1969) which secured it are perhaps the most defining events, and indeed the seminal ones, in modern Japanese history. It began as a rebellious movement of the western feudal domains of Satsuma, Choshu, Tosa, and their allies against their overlords the Tokugawa Shogunate (1603-1868), a military regime that had ruled Japan for 250 years and was heir to a longer tradition of Shogunal rule dating to the 11th Century. From a purely military perspective the turning point of the conflict was a series of maneuvers, battles and betrayals in the area around Kyoto and Osaka in January and February of 1868 that led to the subsequent Shogunal surrender at Edo (modern Tokyo) on the 8th of March. However, perhaps the real turning point had occurred before hostilities even broke out in November of 1868 when the Emperor Meiji declared a restoration of his own direct civilian rule. This move prompted by the western rebels, combined with the subsequent formal abolition of the Shogunate and confiscation of Tokugawa lands challenged the military establishment’s raison d’être, legitimized the rebel forces, and conversely made Shogunate loyalists into rebels of a kind themselves.

The Shinsengumi, as an irregular force partly composed of ronin - a highly romanticized status in Japan even before the Restoration- outside of the normal hierarchy and forces of the Shogunate (itself the focus of Imperial displeasure in the victorious Sat-Cho Alliance's worldview) were somewhat easier to rehabilitate as 'honourable rebels' in the post-Restoration era due to this slight distancing from the Tokugawas. Conversely, because they were fighting for the Tokugawas, and thereby adhering to a feudal loyalty (the only legitimate form of loyalty beyond that to the Emperor for soldiers), their rebel status was viewed as honourable where that of subsequent non-military rebels against the Emperor were not.

After the conflict, the leaders of the victorious rebel domains sought to establish a new national polity (kokutai), ostensibly under the direct rule of the Emperor but in reality firmly in the hands of a few elder statesmen (genro) drawn from their own ranks. Successful rebels themselves, these samurai-turned-statesmen, in attempting to centralize and modernize what they saw as a backward state and economy faced opposition and dissension both from the outside and within their own ranks, and soon themselves took repressive steps to maintain the post-1868 status quo.

Turning to other rebels, the instability resulting from further social and economic reforms under the new regime led to numerous rebellions, riots, and uprisings in the Meiji Era but for brevity’s sake we will only examine a handful here. The most significant and most often memorialized rebellious figure during the Meiji Era was undoubtedly Saigo Takamori. A stalwart of Satsuma domain who had played a key role in the Restoration, the Boshin War, and the new regime, the conservative and traditionalist Saigo seemed an unlikely candidate for rebellion. However, following a succession of ‘progressive’ laws that abolished samurai privileges and the failure of several smaller related insurrections, samurai ostensibly loyal to Saigo rose against the central government in 1877, arguably forcing Saigo to become their leader, although his motivations for opposition to central government policies were in reality more complicated. The ensuing sanguinary conflict, known as the Satsuma Rebellion or the Seinan War, was one of the most brutal domestic insurrections in Japanese history though it lasted a mere eight months. After suffering several significant defeats it ended with the surrender of Saigo’s forces following his suicide.

A decade later, however, the Meiji government rehabilitated Saigo with a full pardon and a posthumous restoration of his court rank in 1889. But why take this step for a rebellion and figure that represented the most serious military threat to the new regime? There are several reasons, not least of which that he was a very popular figure both during his life and afterwards. This popularity grew after his death, partly out of continued traditionalist dissatisfaction with the modernizing and Westernizing government, unfounded rumours of his survival, and a growing nostalgia for the ‘good old days’ of the samurai and bushido values he had come to symbolize by the late 1880s. Essentially Saigo – as a member of the Restoration’s rebel pantheon – was a socially safe example of protest, and was memorialized as a symbol of Japan’s rapidly fading warrior past. Feudal loyalty, loyalty to one’s lord and domain, was seen as second only to loyalty to the Emperor for the samurai of Saigo’s generation, and rebelling to defend or maintain one’s feudal obligations was seen as honourable in a way that other challenges to Imperial authority were not at the time. And finally and perhaps most importantly, it is important to note that that when Saigo and his followers rebelled in 1877 they did so not against the state or Emperor, but against the dominant faction of the Meiji government in the name of the Emperor, just as the founders of said government (Saigo among them) had in the 1860s.

This view of Saigo made his rebellion righteous, justified his rehabilitation, and cemented his place as a significant, though often popularly and ideologically misrepresented figure in Japanese history who set the paradigm for the image of a post-Restoration Japanese ‘righteous rebel.’ The scale of the Satsuma Rebellion and the significance of Saigo as a popular and historic figure overshadowed the earlier samurai rebellions and marked an end to similar uprisings. It would however have a significant impact of how subsequent acts of rebellion were viewed in the Meiji Era and well into the 20th Century.

Disregarding a few small-scale mutinies that were quickly repressed with little fanfare, most subsequent protests, uprisings, and opposition movements of the Meiji Era were distinct from the Satsuma Rebellion in that civilians instigated them. One early case of note is the Fukushima Incident (1882), a campaign of tax resistance and proposed civil disobedience relating to the imposition of corvee labour led by the Jiyuto (‘Freedom and People’s Rights Movement’) in Fukushima Prefecture that was violently suppressed by government forces who murdered 51 organizers in their sleep on the 18th of August, 1882. This was only one of a number of similar peasant uprisings – including the subsequent Chichibu Incident (1886) – involving the Jiyuto, liberals whom the Imperial government suspected of having republican tendencies and despised as potential traitors in a way they would never have viewed Saigo or his samurai comrades who had ostensibly rebelled for the Emperor. Similarly violent disregard for civilian protestors was evident in the suppression of urban rioters in a number of incidents between 1905 and 1918, notably including the Habiya Incidiary Incident (1905) in the late Meiji Era. In addition to popular protests and riots later Meiji governments singled out anarchists and socialists. Of particular note is the Taigyaku Incident (1910), an alleged anarchist and socialist plot to kill the Emperor that resulted in the execution of twelve ‘conspirators’ and the imprisonment of others. This incident and others like it were widely publicized and created an atmosphere of fear among the Japanese ruling elite which led to a series of expanded repressive measures culminating in the so-called ‘Peace Preservation Laws’ which suppressed dissent and contributed to the further growth in the Japanese military’s political power after the Meiji Era.

Unlike Saigo Takamori and his samurai or the Shinsengumi, these rebels and protesters were never formally rehabilitated in pre-war Japan, and despite the adoption of some as predecessors by post-war Japanese leftists and the work of Marxist historians none of them have the popular cachet today that Saigo does. Considering this, it seems clear that there is a double standard at work regarding Japanese rebels, with ‘honourable,’ often socially high-status military men being viewed as acceptable, or even as heroes, and with all others, especially those of low social status or those engaging in party politics (especially those on the left), seen as ‘dishonourable’ traitors to the nation, the state, and most importantly the Emperor.

I attribute this double-standard for rehabilitation and celebration of rebels to various political factors relating to modern Japanese civil-military relations in my paper. If you are interested in my sources or want to read the whole thing message me your contact information and I can send it to you. It's a very interesting topic.