My first reaction was this: it does save you the work of stimulating them yourself!
That was not my favorite orphaned kitten job!
But after thinking about it further......I wouldn't worry about the puppy having problems with this (unless the kittens have worms and those could be passed on), I would be more concerned that you lose the ability to monitor the kittens waste. Orphaned kittens can be pretty fragile, and the color/texture of their waste could be a sign of potential illness.
I wouldn't stop the puppy from doing it (in fact the only way to stop it is to entirely separate them), as it will build a bond between them. But I would monitor them closely and limit how often he/she does this. Be prepared to deworm the puppy if you find out the kittens have worms.