The legal complaint (via GameStop) indicates that this isn't simply an issue of the same name being used. Rebellion asserts that the text of "Rebellion" on the Sins of a Solar Empire logo is larger than the rest of the text. This goes hand in hand with the fact that Rebellion (the company) always use "Rebellion" in larger than life lettering.
Hence the confusion amongst gamers.
Digging a bit deeper, it also notes some reviews both in text and video formats that refer to the game as "Rebellion" and often mistakenly attribute the game to Rebellion Developments.
If you weren't confused before, you probably are by now.