Chris, I know what you mean. I wanted the Pocahontas cars, that only come with the Warrior steam engine, but I wanted to run them with the Shasta locomotive, and I had no interest in the Legionnaire cars that come with the Shasta. I ended up getting both sets; preferences like that can get expensive.
As Seafold suggests, your best bet may be to get the set at the best price you can, then sell off the loco you don't want, you will probably do as well or better than having a dealer split the set.
An alternative would be to look for vintage Pocahontas cars instead of MTH?