I've never tried it, but I believeTukey mentioned in his book that in the 18th century New England fruit enthusiasts used quince rootstock successfully by burying the root well below the graft union and generally were able to get the benefits of the dwarfing in spite of soil contact with the scion. He didn't mention anything about pruning roots from the scion to make this possible.
One could also protect quince the same way I protect tea roses- by piling up soil against the trunk during winter and pulling it back in spring. I used to do this with betufolia but I've grown lazier and haven't paid the price- no test winters lately.
[NAFEX] quince in cold climates,
Alan Haigh, 08/13/2010