Is it ok to cut the USB 3.0-specific lines on a USB cable?
Yes. It would be like they were never connected. You do compromise the effectiveness of the shield around the cables by cutting it though, so try to minimize that or ensure you tightly tape it back up.

But couldn't you use a 2.0 cable in the first place? The usb 3.0 micro b connector has two parts, a 2.0 micro b five pin part and a newer 3.0 only five pin part. A usb 2.0 micro b cable can plug into the corresponding side of the 3.0 micro b jack for 2.0 and power only access.