I have no idea whether a screen protector would interfer with the touchscreen. It'll almost certainly detract significantly from the visual quality of the screen by adding glare or murkiness, which makes the point of getting an E-Ink device somewhat moot.
I know this doesn't answer your question, but I'd consider getting/making a cover instead. I have an invisibleshield on my touchphone, it works well, but I would never put something like that on my reader. The screen is designed to withstand regular use of a stylus or finger, a soft cover will add very little bulk to your device, and it doesn't hamper you in everyday use.
A tip: I usually keep my reader in a soft cover in my jacket or backpack pocket while travelling, then I'll just fish out the reader while leaving the cover in the pocket. I basically employ the cover as a lining for wherever I keep the reader while not using it. This subtracts about 2 seconds total from a single reading session when I replace the device in my pocket.
I've never been in a situation were the screen was in danger of being scratched while reading, even when being jostled around standing on a full bus
