How to remove soft navigation keys in Xperia without affecting Dialer's call button?
Try hiding the soft keys using Gravity Box, a module for the Xposed framework. Gravity box will let you tweak parts of Android without the need for a custom ROM. There are 3 different versions of Gravity Box for 3 different versions of Android (JB, KK and LP). Link for framework: Xposed. Link to modules: Modules. You can then search for the module you want.