Well, Minecraft being written in Java is a special case since it is easy to decompile and modify Java programs. But even that, AFAIK Mojang didn't try to avoid mods, they just couldn't come up with a good mod API themselves. If anything they are also pro-mod, which kind of supports what i said :-).

I mean, it isn't like there aren't other mod friendly engines, they just tend to be a small minority and they tend to be older engines (e.g. another engine that comes to my mind being very mod friendly is Aurora Toolset and its derivatives, like Electron, Odyssey, Eclipse and to some extent Lycium, although Bioware didn't release a toolset for the last one).