I mean, Maul being Empire would be like Rebels having Access to Darth Vader because he was redeemed at the end. And about as sensible as the Rebels just letting Vader waltz around on their ships too, considering that Inquisitors and big V very explicitly tried to kill Maul in the GCW timeline to say nothing of that one time ol' Sheev himself tried to kill him and stabbed his brother .
Very briefly, Maul was a sith apprentice with a Darth title, working for the guy who would eventually become Emperor, manipulating the Trade Federation like 20 years before the Empire became a thing. Then he was revived by a third party who ultimately opposed both CIS and the Republic, and he built a criminal cartel and occupied Mandalore, which had to be besieged by the Republic (this is why the Empire occupies Mandalore later). That's categorically scum, and strongly anti Republic and anti-Empire. Presumably he is then chased around by the Inquisitorius for the next 6-8 years however long until Rebels. He's not even properly "Rebel", he can only be linked to a list with Ezra, because Ezra is an idiot who tries to learn from weird, hooded and tattooed men he finds in ancient Sith ruins. Even Ezra ends up opposing him, but dropping the "or Ezra Bridger" restriction would mean waiting longer to release Maul and make him less interesting. Good that they try piloting some of these mechanics sooner rather than later.
If there was a Clone Wars era/factions to this game, sure, an argument could be made for him as a CIS pilot (same as BFII), but since we don't go back that far, it's all nonsense .