I manage to protect Joya with a faily good success :
- I position her behind geoffrey, midlane most of the time.
- I try to avoid first and last lane which are often taken by powerfull cross-attacks from my opponents (stratus, azrael, etc...)
- Cryptor does help keeping her alive too.
As for Joya vs FD
To my experience FD is better weither you shoot first or second as a locked Joya is still weaker than a locked FD.
Go for Joya only if :
You want to spare money
If you other commanders can protect her cause she will deal strong and steady dmg in that case