Return to Answer

Partial answer

(I have decrypted all the messages. Some further reasoning is required to figure out who's who. I'm in the middle of something else right now and will return to this later.)

So, so far we know

Ettore E -- known Mazzini links, though I don't know that that guarantees he's our Mazzinist.
Michelle M -- not plotting to assassinate the Empress. Likely funded from Bavaria (German kingdom).
Benoit B -- Russian connections, apparently actually called Misha (= Mikhail), no obvious plotting in message.
K89 -- possibly Marxist, backing from Belgium, not Bakuninist.
Brumaire -- not Bakuninist.
Bomb plot -- backing from Britain.
Pantagruel -- male (so not Judith J), not Blanquist, not funded from Italian state, not Marxist.
The Blanquist -- funded from Sardinia, an Italian state.

You should arrest

everyone except Benoit, probably going after Michelle first for your own safety and then Judith because of the severity of what she is planning to do. ("The female of the species is deadlier than the male.") You might also want to congratulate Benoit on his forthcoming marriage and promotion.

Let's begin with the decryption.

OK, let's now see what inferences we can draw. First of all,

I'm going to take it that Benoit B = Misha, the recipient of message 2, is not any sort of revolutionary despite his use of at least one false name, since apparently he is considering taking up a position at the Russian court. I'm not sure how justifiable this is, but I think we need it in order to get a solution. I think we also need to assume that no one is lying, no one is a double agent, there aren't any plots afoot other than the ones we know about, and words like "father" and "daughter" and "wedding" mean what they say rather than being code for other things. Maybe we can also assume that "Benoit"'s innocent communications with Russia are a complete explanation of the suspicious communications with that nation, so the other four nations mentioned are the ones we need to worry about.

Now

the "Marxist man" (4) is not Benoit; neither is he Ettore, who is a known Mazzinist; so he must be Hans. (The other two suspects are not men.) And now Pantagruel, a "proud father" (4) and hence also a man, must be Ettore, the Mazzinist.

There is

a Blanquist plot funded from Sardinia. This can't involve Benoit (deemed innocent) or Michelle (whose associates are in Bavaria) or Ettore (who is a Mazzinist) or Hans (who is a Marxist). So this one is Judith.

At this point we know that

Ettore is a Mazzinist, Benoit is innocent, Hans is a Marxist and Judith is a Blanquist. Therefore Michelle is the Bakuninite anarchist.

Now, Michelle

is not plotting assassination (message 1), pamphlet-smuggling (message 3), or extracting fugitives (message 3). So she is the one with the bomb plot.

And K89,

with the pamphlets and the Belgian connections, is not Ettore (who is Pantagruel) or Benoit (who is innocent) or Michelle (whose connections are Bavarian) or Judith (whose connections are Sardinian). So this one is Hans, the Marxist. Now we've assigned countries to everyone other than Ettore, who must be the one with British connections.

This means,

by message 3, that Ettore is the one helping fugitives escape, and now we've assigned plots (or absence-of-plots) to everyone but Judith, whose Sardinian-funded Blanquist plot is apparently the assassination.

At this point the only thing we haven't figured out is a couple of the codenames:

Michelle and Judith are Norbert and Brumaire. But from message 3 we know that Brumaire isn't the anarchist, and we have found that Michelle is the anarchist. So Judith is Brumaire, and Michelle is Norbert. (Should it be surprising that Norbert turns out to be female?)

And now we know everything:

Ettore, also known as Pantagruel, is a Mazzinist running a British plot to smuggle fugitives out of France.
Benoit is not involved in the plots; he is a Russian nobleman travelling incognito, which explains the suspicious communications to and from Russia.
Michelle, also known as Norbert, is a Bakuninite anarchist funded by Bavarians, plotting to blow up the town hall.
Hans, also known as K89, is a Marxist with Belgian connections plotting to smuggle subversive literature.
Judith, also known as Brumaire, is a Blanquist funded for unknown reasons by some Sardinians in a plot to assassinate the Empress, a plot that even the anarchists regard as unwise.

Some stereotypes are confirmed here:

the anarchists are running a bomb plot, Brumaire belongs to a specifically French revolutionary group, and the Marxists are the ones calling one another "comrade".

Michelle M -- not plotting to assassinate the Empress. Likely funded from Bavaria (German kingdom).
Benoit B -- Russian connections, apparently actually called Misha (= Mikhail), no obvious plotting in message. K89 -- possibly Marxist, backing from Belgium, not Bakuninist.
Brumaire -- not Bakuninist.
Bomb plot -- backing from Britain.
Pantagruel -- male (so not Judith J), not Blanquist, not funded from Italian state, not Marxist.
The Blanquist -- funded from Sardinia, an Italian state.

Ettore E -- known Mazzini links, though I don't know that that guarantees he's our Mazzinist.
Michelle M -- not plotting to assassinate the Empress. Likely funded from Bavaria (German kingdom).
Benoit B -- Russian connections, apparently actually called Misha (= Mikhail), no obvious plotting in message. 
K89 -- possibly Marxist, backing from Belgium, not Bakuninist.
Brumaire -- not Bakuninist.
Bomb plot -- backing from Britain.
Pantagruel -- male (so not Judith J), not Blanquist, not funded from Italian state, not Marxist.
The Blanquist -- funded from Sardinia, an Italian state.

is decoded as follows: write everything in (modern) Morse code, take just the first symbol of each letter, group those together by words and interpret as Morse letters. We get: "Misha -- Cousin Fyodor is in Paris. Father consents to wedding on condition that you interrupt your travels and accept a position at court. Please consider immediate return to Saint Petersburg. Yours, Kolya." So perhaps Benôit B is actually a Russian named Mikhail. Does that help us? He can't literally be Bakunin, who in 1858 was in exile in Siberia.

is decoded as follows: write everything in (modern) Morse code, take just the first symbol of each letter, group those together by words and interpret as Morse letters. We get: "Misha -- Cousin Fyodor is in Paris. Father consents to wedding on condition that you interrupt your travels and accept a position at court. Please consider immediate return to Saint Petersburg. Yours, Kolya." So perhaps Benôit B is actually a Russian named Mikhail. Does that help us? He can't literally be Bakunin, who in 1858 was in exile in Siberia. At face value the message contains nothing suspicious, though plenty of things here could have secret meanings of one sort or another.