The title is a good indication of the main dilemma of the narrative. A brilliant oxymoron, The Good Terrorist is about exactly that, the moral dilemma of a person who believes her theory to the point of enforcing it herself through small acts of terrorism.
An important feature of this story is that Alice, the well-intentioned terrorist, is only really able to dismantle the bourgeoisie of her own family, primarily through kleptomania, taking valuable rugs to afford her expenses, instead of working of course, and eventually stealing enough money from her father to ruin his already-strained company. Notice that her version of bourgeois includes a failing small-business owner, namely her own flesh and blood, her father. That doesn't protect him from her blatant evil.
The core nugget of meaning might be the moralistic point of view that people should always come before dogma, or perhaps that dogmatic mindsets are counter-productive, because they aren't flexible enough to deal with the unspeakable complexity of daily life.