"Is it fair that those who are part way through paying off their mortgage may find themselves with less of the pie they have been working hard to own?"
Definitely, it would be very fair
The thing, with the negative gearing government subsidy, is everyone else is working hard to pay off the negative gearers mortgage.
That is money that could directly go to income tax cuts.
, your home is a home. don't treat it as an asset. Its somewhere to live.