Here are the bunch of options you can try .. see if they work for your scenario
1. "presence privacy mode" option
2. Creating OU without syncing with O365 Groups
3. In AD setting the value for msExchHideFromAddressLists
These options were discussed in this thread ...
https://techcommunity.microsoft.com/t5/Skype-for-Business-Users/Hide-User-from-Skype-for-Business-On...let me know if this helps!