Well, for now we have to live with what FCKeditor provides unless someone makes a plugin for FCKeditor that does it better. The thing about it is, its a moving target, as soon as any obfuscation technique becomes widely used the spam bots find a way to crack it and it becomes less effective. ROT13 look promising, but just like captchas, eventually someone will break it and then someone will come up with another technique.
From source view, you can use whatever technique you wish.
Best,
Joe