Certified GKH Gardening Expert
You can kill the stumps by drilling holes into the stump and pouring Round-up into the holes. Repeat every few weeks to make sure it is dead. This will at least stop it from growing further into the drain lines.
I personally like to use a sawzall when removing stumps. You can plunge the disposable blade into the soil around the stump and cut through any roots. Then just lift the main part of the stump out.