I realize this is a very old thread, but I wanted to reply to it as I did find the way to change the mappings for this. If someone could sticky this for future users that would probably be good as I'm sure there are other people wondering about this.
Navigate to the folder in C:\Users\YourUserFolderHere\Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion\Settings
You'll note this is exactly the same as the previously mentioned step. Here's where we diverge and actually fix the problem. Open up rebellion.uimappings.setting You'll want to right click it, open, click the bubble that says "Select a program from a list...", and click ok. Now find notepad, and UNCHECK "Always use the selected program to open this kind of file"
The two entries that you want to locate are: CURSOR_BUTTON_1 and CURSOR_BUTTON_2. Their code should look like the following:
CURSOR_BUTTON_1
NumMappings 1
Mapping
Device "MOUSE_BUTTONS"
DeviceInputID 1
isAltDown FALSE
isCtrlDown FALSE
isShiftDown FALSE
CURSOR_BUTTON_2
NumMappings 1
Mapping
Device "MOUSE_BUTTONS"
DeviceInputID 2
isAltDown FALSE
isCtrlDown FALSE
isShiftDown FALSE
Once you have found these two entries, what you want to do is change "DeviceInputID 1" and "DeviceInputID 2". Just swap them. Now, CURSOR_BUTTON_1 should have "DeviceInputID 2" and CURSOR_BUTTON_2 should have "DeviceInputID 2". If you want to completely disable the rotate camera functionality, just remove "DeviceInputID 1" from either one (I think, not tested so use at your own risk!). Personally I think you should keep the rotation functionality just in case you wanna peer around something, but having it on right click WAS very annoying.
I hope this helps anyone else who did endless amounts of google searching as I had done. Enjoy!