If it's more efficient for your business/project to change your URIs when going through a website design, go ahead (with the knowledge that you'll lose some traffic, etc.)
Seriously, there's no reason to feel guilty over this. It's not your fault, it's the fault of a system that built two UIs into every website (the website's HTML and the URL bar -- the second of which is supposed to be useful for browsing and navigation just like the first).
If W3C actually cared about links continuing to work, they would fix it at the technical level by promoting content-addressable links instead of trying to fix it at the social level (which will never work anyway, the diligent people that care about these things will always be just a drop in the bucket).