characters - Is it okay to write a story where the protagonist is a Terrorist?

I am writing a side story called, The Afterglow of Jovian, which mainly takes place sometime during the final stages of the main story. Here's a brief gist of the main story to give some context,

• The main story takes place in the future, 566 E.A.E.


• By this time mankind has successfully colonized most of the planets and moons in the Solar System.


• Due to the immense success of colonization and terraforming, from the end of the year 2099 A.D there was an exodus from Earth.


• Thus 2100 A.D is officially marked as the epoch for the start of E.A.E (Exodus: After Earth) era.


• Eventually, a global government called the Third Planet Alliance is formed as a form of a global government.


• The main story follows Lisa Roberts who is part of an elite counter-insurgency unit called the Titans, who are tasked with neutralizing the terrorist faction known as Jovian Liberation Army.


• The Jovian Liberation Army are a military resistance coalition formed between the moons Europa, Ganymede and Callisto of the Jovian system.

The main story, as mentioned above, mainly focuses on Lisa Roberts and the Titans neutralizing and eliminating the terrorist faction. In my side story, I am thinking about telling the story from the terrorist faction side. While in the process, I am also thinking of exploring more of the backstory and the reason for the uprising of the Jovian Liberation Army.

My only worry is: Is it a good idea for the protagonist to be a terrorist? Generally, people don't like the word "terrorist", due to the negative connotation associated with the word. And, it is generally also frowned upon in society. Because of this dilemma, I am also thinking to introduce a secondary main character who at one point, during the very early years of Jovian Liberation moment, was a former Titan member. But, he becomes disillusioned with the Third Planet Alliance government when he is ordered to gun down the severely undermanned and unharmed Jovian resistances soldiers. I am thinking this might help the readers to connect a bit at least.