I have been trying the same and running into the same exception. From experiences in the past I think it is not unlikely that although Goko is java based some ARM specific build settings need to be set to apply during the build fase to make it run on the RPI (raspbian stretch (Debian based)).
The RPI hardware architecture differs from x86 and especially C(++) software needs to be compiled with the correct compiler variant otherwise it just will not work.
At the moment I use CNCjs but as I am looking for a way to have all components for an item (for example a cabinet) milled in one batch (like top, bottom, sides, back, door, etc) out of a sheet of plywood), I am testing other options. Looks like Goko as it is now provides a lot of useful features to do so and therefor a strong candidate. My set up now is an RPI 3 hosting CNCjs and an Arduino Mega running Grbl. Because of the small footprint of the RPI and the low cost I like to keep the RPI in the configuration.
Tinkering away I installed Eclipse on top of Raspbian stretch but importing the Goko project results in a long list of errors. Reading through the forums etc it is clear that you use a specific Eclipse bundling (RPC and RAP), I would be surprised if this bundle is available for Raspbian but I will look into this as well if it is possible to cross-built (cross-compile).
As the batching of multiple g-code files is off importance to me I my help to 'port' Goko to the RPI Raspbian platform and assist in developing functionality to support basic nesting.