The exhaust should hang from the frame instead of the body, so removing the hanger at the e-brake mount would be a good thing to do either way. It sounds like the PO was just trying to take a shortcut. The first hanger in the system is usually on the outlet side of the muffler, so it seems a little too far forward anyway. If you have a hanger near the muffler outlet, you shouldn't even need to replace it.
As for the routing of your pipes, it sounds like you're right. Normally, the exhaust goes below the e-brake lines. If your pipes are too close to the mounts you'll have to move the pipes or the mounts.
I think the best thing to do would be re-route the pipes to a more standard location. It will be easier than redesigning the e-brake system, and it should lower the temperature of your floorboards.