WIP limits shouldn't be rigidly enforced. Instead a warning should show when you are over WIP, and some stats gathered in the background. If your team goes over WIP occasionally, it's usually fine. If you go over WIP a lot, your process is broken somehow. How, when, who and where you went over WIP can give you a lot of info on where your bottlenecks are and how to improve your process.

I've been on a Kanban team for the past year now and I can say with confidence that if our tool didn't track WIP, we would be less effective as a team.