First How to Just Unroot the Device
You can unroot the phone by opening SuperSU app and choosing full unroot (or just removing /system/bin/su is sufficient usually, and can be done with a file manager like ES File Manager (left hand tray has tools header and under that is the root access toggle and Mount R/W tap that and select /system to be rw) you can then delete the su binary in /system/bin (sometimes /system/xbin though this is more rare)).
More Detail and possible solutions [First Guest Account]
I do not know of any direct ways of hiding SU from apps, but you could try a guest user and if you leave the multi user option in SuperSU unchecked then the guest user account may be able to run the app and the app may not see the root.
More Detail and possible solutions [Second Unroot then use Custom Recovery to Apply Root when Done]
You can lose root and be OK if you maintain the custom recovery. Then what you could do is do full unroot from inside SuperSU app and restart device. Now install and/or run Pokemon GO!. When done restart to recovery and flash SuperSU.zip and restart again. Now you will have root access back until next time you wish to play Pokemon GO!.
Editorial [some Concern for Users from the Author]
Now you do realize Pokemon GO! was done by an NSA contracted company and is used by the government as a general spy tool (think about it a bunch of people running anround with phone cameras and mics running is a wet dream for those guys), so you may want to re-think what games you play and what permissions you are allowing apps running on your devices to use (same guy that designed Google Earth Originally for the CIA/NSA before Google Bought it and same guy who wrote the Game Ingress that was originally done by a company under direct CIA contract before Google bought them).
Reference [I'm not just a conspiracy theory nut without backup proof ;-)]: