The terrorists are entirely justified in their violent resistance against the obviously evil and genocidal Britannian empire, which is something of a stand in for both the British Empire and the US.
The annoying liberal deuteragonist bumbles around for 2/3 of the show being a supersoldier for the Britannian Empire while constantly making these bizarre self righteous arguments that Lelouch's rebellion is just too darn mean and violent, we have to support the Britannian Empire's rule of law just a while longer guys! The longer this goes on, the more and more his world view crumbles around him as basically nothing goes to plan for this liberal who is just incapable of grappling with material reality. He ends up following his sense of liberal morality all the way to accidentally killing millions with a Britannian wunderwaffe nuke. This leads him on his jokerification arc wherein he realizes the error of his ways and actually supports Lelouch through the batshit last few episodes of this show.
Anyway, I can't recommend this show to anyone in year of our lord 2024 because it's obnoxiously, embarrassingly horny in a very mid 2000s anime way, because that's exactly what it is. But I'm imagining what could have been.
There is two problems with this conflict though. Firstly, the way that Lelouch built a resistance against his brother was not to win back his old allies and prove to them his trust worthiness, but by magically flip the whole chessboard and turn every Britannian into a mind slave willingly do his bidding. That sounds exactly like liberal fantasy fixing the system and transform it into a force for good. Secondly, Schneizel also did a board flip and get everyone on the rebel group to support him as their leader for a war which essentially is just a fight for the throne of the world. The rebel even complicit in a nuclear first strike attack on the Britannian capital which have unknown number of civilian in it.
This plot point however shine the spot light on the structural problem of the whole rebels. They are just a bunch of people with no unified ideology that can let them look pass the fear of the power of geass to even offer Lelouch a chance to explain himself. They don't even offer him a real trial before trying to gun him down in cold blood. While I'm sure there are many example in real life where people flipped out and assassinated their political leaders for less. The story decision here to let Lelouch be saved not by the quality of his ideology, or any of his policies but just purely because another broken and exploited character clung onto him and bailed him out with their life speak a lot for the quality of the rebels leadership and ideology.
That's my main problem with Code Geass to be honest. Overall, it's an entertaining show with the facade of anti-colonialism, anti-imperialism, pretty twisting story line and some awesome mecha battle. However, the show stop short of offering any true solutions to the problems and instead just outright prescript great person theory and enlightenment dictatorship to imperialism. It doesn't even have any representation for communism, anarchism or any more leftist groups. Instead, we had an imperial capitalist monarchism vs a bunch of nationalist monarchist of a different religion vs some liberal democracies in the background.
I agree the show, especially toward the end, is definitely no kind of masterpiece, and many of the plot points are definitely really dumb, just in a very entertaining way. You're correct that the fact that Lelouch almost died because his cadres didn't have a real shared ideology that would allow for them to have any kind of faith or respect in his leadership doesn't quite work as a criticism of exactly that kind of organization when Lelouch uses his geass to win anyway by mind controlling the remainder of the Britannian Empire's armed forces.
My being impressed at this show mainly comes from the mere fact that it's very explicitly and wholeheartedly endorsing violent resistance against US coded imperialism. I feel as if that's rare from popular media, especially back when it released. It neglects to take a specific political stance, but it's absolutely anti-imperialist, even if just being that is a low bar to clear. The rest is mostly very fun but harmless anime slop apart from the parts I criticized in the OP.