I traveled under my parents passes years ago, so not sure if this is still relevant.

I see no issue with you booking two separate tickets JNB-FRA and FRA-EWR, since you can break the journey as they are space available anyways, you're not taking away from inventory. Assuming of course you're allowed to enter Germany. Edit, we did this all the time with my parents passes, and traveling on SpaceA OAL tickets. But I was always traveling with my parents.

Although I'm not sure how you're going to fly on LH when you're not the employee, but I don't remember all the rules with ID90s.

When flying, make sure you adhere to the dress code, and the rules. Whatever you do, do not under any circumstance, create an issue with anyone (flight crew, gate agents, pilots, ground staff, etc.) It will be written up and your friend might get in trouble, fired, or lose their pass privileges. They take these things very seriously. Just be polite and compliant.

Lastly, if your friend is a new employee, priority is determined by seniority, vacation passes, etc. So you will likely be on the bottom of the standby list. Be prepared and expect that you will be bumped, so have a back up plan. It's very expensive to fly back from ZA to the US. Even empty flights have risk of being denied boarding.