I don't think Ditko was setting up Gwen Stacy to be Peter's girlfriend. But I'm not so sure about Harry's girlfriend either. I honestly believe he was setting up a female antagonist for Spider-man. Perhaps a love interest too, but in the old school Batman/Catwoman sense. I don't think it was a coincidence that he depicted Gwen dressed in red with high arched brows and devil horns in her hair. She looks and reads like a classic femme fatale.
Attachment 128972Attachment 128973
Unfortunately for her she ultimately ended up being a femme fatality.
As far as Ditko's plans for Mary Jane, it's possible. I think it certainly reads that way. But unfortunately we'll never know for certain because (as far as I know) Ditko never spoke publicly about his plans for those characters.