In my opinion he did play a role in the creation of the Minors, at least in some which he considered more important. The Two of Cups and Ten of Pentacles are often cited as examples of his more obvious handiwork, but I feel that in cards such as the 2 of Wands; 4,5,7 of Cups and 2 of Swords all betray at least elements Waite would have told Smith to include.
The globe, for example, on the Wands card doesn't seem, at least subjectively, to be something that would be on the card unless the decks's background is considered, and not simply a device came from being given meanings to work with. The Moon on the Swords card, unobtrusive as it may be, actually makes the whole picture since it is the only example I can think of that the astrological attribution is displayed, making the whole card an astrological glyph. Heck, even the island looks like Libra.
There are more examples, and this is without even going into Mary Greer's findings on the Masonic symbolism involved. I don't think the creation of the Minors was any kind of extreme, either with him dictating them or her working alone. I don't think their partnership was anything as close as that of the Crowley/Harris one, but PCS certainly wasn't working in a vacuum. I don't know why he would choose to downplay his involvement in a large part of his own project, though.