I think you have a legitimate concern. I would have the home seller include a home warranty with the sale to deal with any short term heating/cooling problems that may arise. Also, with any older home you will run into upkeep problems and things you will want to change. I would have some funds set aside for this and include it in my buying budget.
When the housing market stabilizes I think you will see the market times coming down to a reasonable level. But seeing long market times now is a fact and I would only make offers that address the relocation issues. If you are set on your older Victorian/Queen Anne home you might also look at Downer's Grove, the price point might help in your relocation fears.