I read somewhere a long time ago the only difference between a freedom fighter and a terrorist is whether they’re on your side or the other side. For the sake of this post/discussion, let’s go with that definition, m’kay?
What I’m wondering about is there a emotionally neutral word for this type of warfare? “Partisan” strikes me as a bit on the pro side. Would “guerrilla” be considered neutral or is there a better word someone here can come up with? 
Militant?
Guerrilla refers to a specific kind of tactics, so not every ff/t is a guerrilla fighter.
I think it’s a matter of citizenship and who’s occupying whom.
If outside influences get fighters to attack citizens in another country, they’re terrorists, even if some of them are citizens.
If citizens are attacking outside influences who are occupying the citizens’ territory - they’re freedom fighters.
If citizens are attacking fellow citizens within their own territory, then it’s domestic terrorism and/or a civil war.
Rebel, resistance fighter, militant, revolutionist, insurgent, renegade, insurrectionist
Rebel, militant, and renegade all have negative connotations. Resistance fighter is a fairly positive term. I doubt many Americans would decribe ISIS as resistance fighters, even if the term is technically accurate.
Revolutionist or insurrectionist might be regarded as neutral, insofar as I’ve never heard anyone actually use those terms.
Sectarian violence? Paramilitary?
Or even just “irregular forces”.
Ben Franklin, from 1776: “A rebellion is always legal in the first person, such as ‘our rebellion.’ It is only in the third person - ‘their rebellion’ - that it becomes illegal.”
I like this analysis but some moron will come along shortly to twist the meaning of “occupying” to include “influencing culture”. You can see where that will lead.
Irregular warfare, unconventional warfare, uprising, rebellion, Revolution, and insurgency are all terms that could be applied to particular circumstances. However, they are not all synonymous.