Sorry to hear about the name conflict. We weren't familiar with the patch sets manager. If it helps to keep the quilt (data) command line tools out of your path, you can still run all the quilt commands from inside Python.
Quilt is an incredibly widely used tool. Many kernel developers use it as an alternative to git for patch management, and it's used by most distributions to manage their patches on top of upstream projects.
No worries, just make the name switch sooner rather than later. Since your target audience is obviously developers in general - to whom the patch tool is well known - it will most likely affect your business negatively if you don't...
How did this not come up during your market research?