Hi - thanks for trying it! I don't think that worked quite right, though. Let me clear the steps up a bit, so hopefully we get on the same page.
First of all, what you actually want to do is replace the JavaApplicationStub executable file in the Starfarer.app/Contents/MacOS directory with one under /System/Library/Frameworks/JavaVM.framework/Resources/MacOS/.
The first question is, where did you put Starfarer on your system? Assuming it's in the Applications folder, what you want to do is run the following as a single, one-line command from Terminal:
cp /System/Library/Frameworks/JavaVM.framework/Resources/MacOS/JavaApplicationStub
/Applications/Starfarer.app/Contents/MacOS
It wraps around in this post because it's too long, but needs to be a single command when you type it in - that is, type/paste the whole thing in without hitting enter.
Once that's done (and again, assuming Starfarer is in the Applications folder), you'd need to run these two separate commands:
cd /Applications/Starfarer.app/Contents/MacOS
./JavaApplicationStub
If that successfully runs the game, you'll be able to run it normally from that point on. If you put it somewhere other than the Applications folder, it might be easier just to move it there before doing these steps. By the way, would you mind telling me what version of the OS you have?