As I said on IRC.
It won't work. There are 2 dependencies in Apktool that won't work on Android. Yaml and some java 7 code.
Thats why it works fine on Java, but not in Android environment. Bug for java7 code, and the bug for Yaml.
Yaml is only used for parsing out the apktool.yml
file, which is needed for recompile. Java 7 features were introduced for SmaliDebugging and NIO2 aids. If neither are needed, you could recompile the apktool binary without those two. (Of course then missing those features)