I have no idea how much African history Joss Whedon knows, but I think it's fairly unlikely that he knew much about the the Second Anglo-Boer War while he was making Firefly. This is funny, as he managed to replicate it quite well in the war that forms the bulk of the series backstory. He claims to have based his plot on the US Civil War, and the Wild West visuals flow nicely out of that. But he changed enough that the comparison doesn't really stick.
The Independents hadn't been
established Alliance members who split, like the Southern States opting
to divorce themselves from the Union they'd been part of all along.
Rather, the Indeps were those who'd physically left Alliance space to
find new worlds of their own. This makes them more similar to the Dutch settlers who eventually became
known as the Boers (literally, farmers), who left the Cape Colony after
Britain gained control of it (similar to how the Independents left the
Core planets behind to the Alliance) and went on to found the Natalia Republic (conquered by Britain in 1843), the Orange Free State and the Transvaal Republic (both in the bag by 1902), as well as half a dozen brief little micro-states. A huge clue to their motives lies in the name Orange Free State.
The Alliance, therefore, was not acting to
maintain its own historic territories, as the US was in 1861, but was instead
aggressively invading neighbours to take their stuff and tell them
what to do, same as Britain did. It's easy to see why Whedon
changed things in that direction: The underdog is easier to get behind
when it did nothing to provoke aggression and is instead just picked on
by a big meanie. I'm not sure I'd call the Union "good guys," but I find
the Confederates even harder to sympathise with, not least because of
the slavery thing. (That's something Firefly skirts around, refering to
it from time to time, without dipping either side in it too obviously. Slavery is just a generic Bad Thing.)
Of course, there are bits of SA history that don't match up with established Firefly canon, like the
People Who Were Already There. The Boers were only the innocent
underdogs in relation to the British, but before that, they'd cut - with a
fair bit of bloodshed - their free republics from various African
nations that were there decades or centuries before them. The Independents, on the other hand, seem to have been the
first to land on their virgin worlds.That might make for an interesting bit of fanfic, a future comic or, dare it be dreamed, an episode yet to be made: Conflict on a Rim planet between settlers who'd arrived in different groups at different times, the early ones who'd initially struggled to conquer the wilderness on their own, with virtually no support from the Core, but still built up significant numbers over the decades, versus the the latter ones who'd arrived with fewer people but better tools and outside connections. If we're using SA history as a guide here, then the war with the Alliance would have been merely a brief hiccup in this longer local conflict.
In fact, that's something about the Firefly 'Verse's history that could be expanded on more generally: Who arrived where, when, and what effect did the order of these things have on the eventual power relations we see in the show. In particular, how did the really early settling of the Core worlds happen? Serenity portrays a single colony convoy departing Earth together, but was that an accurate depiction (considering it came from River's mind), and was it just as simple when they arrived at the other end to set up? If so, then how did the initial conflict arise between the Alliance and the settlers who went out to settle what would become the Independent worlds? Was it anything like the history of the Cape, where there were actually multiple waves of colonists, with different agendas and not much interest in helping each other?
It'd also be neat to see more about the initial formation of the Independents as a coherent group. The Transvaal and Orange Free State teamed up pretty quickly in 1897, but they were just two adjacent states with a lot in common, a single clear opponent and not many other options. But a dozen separate worlds, on far ends of the 'Verse, with probably much bigger cultural divides? Seems like a more interesting challenge.
We'll probably never get conclusive answers, but it's interesting to think about it all, and as I say, always good fodder for future stories, be they official or fanfic, Firefly-related or other.