I'm not sure whether SDL2 will fix this, since afaik ioq3 just grabs inputs as "mouse1", "mouse2", etc. which won't be swapped because you told your DE that you want to use "mouse1" as right click from now on.
The SDL<->OS mapping should take care of this so that the right click (mouse2) is automatically converted into left click (mouse1). SDL would be of little use for input if every game would have to make OS specific calls to check for special key mappings - it would totally ruin SDL's main advantage; platform independency. We know now that SDL2 does it while SDL1 does not, but I would guess SDL1 handles it properly for older systems.
I hope ioquake3 eventually will phase out SDL1.2 and merge the SDL2 branch with their master branch as it seems to have fixed a lot of issues with modern OSes. I think there are more people now that will benefit from the upgrade then the others. SDL1 could still be a separate branch though.
Thank you very, very much!
That worked flawlessly! Not only was I able to compile it, but it also recognises my swapped mouse buttons now!
Great, I am only happy to help + I came across some new and interesting build issues.