Android SSL-TrustKiller does not simply work by putting a new trusted root CA into the trust store since an application could protect against this using pinning, like you do. Instead SSL-TrustKiller patches the SSL-API used by the program so that the usual way of pinning does not work any longer but that the application will not notice this.
While there might be a way to work around SSL-TrustKiller by using uncommon ways to pin a certificate which are not covered by the API patches it is impossible to find a general solution against TLS interception as long as the user fully owns the system (i.e. is root). Such a user could for example modify your application and disable the code for pinning or add hooks into the application to get to the plain text before encryption.