There's no in-game option for it, but you can open the following file and do it manually, by swappping the DeviceInputID values of CURSOR_BUTTON_0 and CURSOR_BUTTON_1:
C:\Users\your username\AppData\Local\Ironclad Games\Sins of a Solar Empire\Setting\uimappings.setting
Please note that some of these directories are hidden by default. To unhide them, go to Control Panel -> Folder Options -> View and set yourself to view hidden files and folders.
