Regardless of the marriage being rocky by the time Diana would have (maybe) been eligible for the GCVO, one thing has stuck out about Diana with me and that when it came to working for the monarchy and the Queen, Diana really wasn't much of a team player. I do have to credit a rocky marriage partially for this because, face it, Charles and Diana were not a team in and of themselves in the first place.
There's been numerous reports that, at first, Diana was reluctant to "do the homework" needed surrounding her upcoming engagements and then, by the time she would have adapted to her role as The Princess of Wales, it had slowly developed into the "Diana show"
The GCVO is recognition for services and support of the monarch and to be real, that simply wasn't Diana's MO. It doesn't surprise me one bit that she never received it.