Old, but perhaps still true …
CyanogenMod’s successor, LineageOS, is working mostly great on the Fairphone 2 and has LED settings where you could turn the LED off for notifications and/or the battery seperately (Settings - Notifications - cog wheel/settings symbol at the top right - LED).
Edit: And there could be something helpful in Gravity Box …
Edit 2: If it is just bothering you at night …