It is kind of obvious that since Goku does not like the whole ´´having to gather a group of ´´every time he needs the transformation, he will undergo training and find a way to use it without the help of others.
Basically the same thing he with his original Super Saiyan Transformation, at first it was supposed to be wild and too powerful to use it for sustained amounts of time, but with training he was able to use it for as long as he wanted WITHOUT the negative side of it, eventually Vegeta,Trunks,Gohan and Gotenks learned to control it the very same way.
It´s Goku after all, constantly pushing the boundaries of his abilities.So in my opinion and based on what he has done in the past, he will be able to go God mode alone by training.
