I've never used that LPE before, but it looks highly configurable. There might be a way to configure it to behave how you want.
However, the Tweak tool has a roughen mode as well. Maybe it would work better? I have used that, and as far as I remember it doesn't affect the original nodes, unless you drag the tool over the nodes. As long as you only drag on the path, I think it only roughens the path. Note that you can set the width of the "tip" of the tool, so that should allow you to get really close to the nodes, without going over them.
The only other option I can think of, would be to duplicate the path before you start, and move it to the side. After you roughen the path, snap the duplicate back in place, and then you can put the end node back where it was originally (using snapping). Then finally delete the duplicate when you're done.
Edit
Also, before we had the Tweak tool and later the LPE, we used the Extension menu > Modify Path > Add nodes, and then Jitter nodes (same submenu), to roughen a path. Note that I almost always get a crash when I use that technique, so be sure to save just before you start. Or use the other tools.