Qantas would be crazy to transfer domestic flying to Jetstar. It would be a classic case of the killing the goose that lays the golden egg. Short haul have been able to make substantial profits (albeit not as much during the GFC) and has made very positive contributions to the bottom line for years. The huge investments made in Qantas Clubs and Business Lounges/Meeting Rooms all over the country imply that imminent transfer of flying to Jetstar seem unlikely.
Sure, the company will try and align pay/conditions to Jetstar (thats hardly new) and Short Haul already have with the launch of Qantas Domestic for all new entrants.
My hunch is all capital city trunk routes remain mainline, all secondary or leisure ports going (have gone) Jetstar.
There is also the need to maintain mainline routes domestically for oncarriage/interline transfers and also as a condition of the oneworld aliance.