The case of recongregators and amalthians is always likely to be the most controversial, since they are the only inquisitor philosophies which directly fit into modern-day philosophies...
I'd argue otherwise, because many others fit with certain interpretations of some religions.
Any terrorist action inspired by religion very much fits with a Monodominant philosophy - "They're not one of us, so they must die."
Thorianism bears resemblance to "Messiahs" in concept, a god born again into another form.
Xanthites - who has never heard the term "fight fire with fire"? There have to be a great many people who look at perceived "enemies" with the intent of giving them a dose of their own medicine. Vigilantism is very much of this kind of mindset.
Istvaanism - this is harder to place, but were the "The US government was behind 9/11" stories true (not a debate for here), then it would have very much have been an Istvaanic action.
They might not be philosophies regarded as acceptable, but they do exist.
Hence I did say 'directly' the examples you've given - while adequate - refer to adaptations of the inquisitorial philosophies (or rather, the reverse). On the other hand recongregation and amalthianism are essentially progressivism and conservativism - two very broad fields - with different names. Also, I might point out that in the modern world, almost all serious politics revolve around these two ideals, with other philosophies being either more refined ideologies within one of these camps (eg. environmentalism, imperialism, liberalism, etc), or having only an importance on a local level, such as messianic beliefs. The closest we get to a 'messianic' state is Israel, and according to their own most fundamental beliefs, they shouldn't actually have gone to Israel, because the messiah hasn't appeared yet!
I should mention of course, that there is really a third broad category that also advocates change, reaction (silly name, isn't it?). This is less popular nowadays, but covers ideologies like religious fundamentalism, and fitted NAZIsm and some fascism too, given their desire to change
backwards. Nevertheless, this was once the most popular theory througout Europe, when people were still looking back with fond illusions to the 'grand old days' of ancient Rome and trying to emulate them. Nowaday, most reaction is in the form of religious fundamentalism and, ironically, what in the U.S. is called conservative. While liberals - around the world - tend towards being very conservative themselves nowadays, having won some ground and not wanting it to slip away.
Basically, there's three options: change 'forward' (towards ideal conditions), change 'backward' (return to established priniciples), and don't change at all. In 40,000, changing backward isn't really in vogue, although I'd reckon there's a fair number of recongregators who would consider themselves to be 'returning the imperium to the emperor's ideal', even if that's not what they're actually doing. This makes Recongregation and Amalthianism the two most open and wide-ranging philosophies of the inquisition, whereas groups like Thorians, Istvaanians, and monodominants have (as a group, not individuals) more narrow fields.
Within both Recongreagators and Amalthians, of course, there are, as previously stated, varying degrees of their ideology. Some recongregators are primarily concerned with small scale clean-outs of corruption, which is a minor progressive (or reactionary) ideal (often claimed by everyone, but usually not pursued by conservatives!). I daresay there are Amalthians more like liberals than true conservatives, seeing minor changes as inevitable only pursuing and terminating movement that might upset their power-base. At the other end of the scale you've got planetary revolution and stuck-in-the-mud proponents of the exisiting order.
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Sorry for the half essay, I guess. Politics is my area of interest (and study), and it's my favourite side to Inquisistor...
-Aidan.