the kernel itself relies on GTK, you can't get rid of it
Really, have you read the blog post I pointed out ? From a standalone application (whatever app you want actually), if you want to train a classifier, just run the openvibe designer (if you use C or C++, system is a good command to start with for instance) with --no-gui flag, then use the player controller to stop the scenario when you need it - it will silently close the invisible designer. Based on what you ask, this solves your problem ; if it does not, then give us more details about the problem.
It takes some time to accurately support the problems users are facing and I proposed a solution to what you stated as your problem, please give it a try.