Hi Sara,
So sorry to hear about all you are dealing with. You've gotten plenty of good feedback from others, so I will not rehash what others have said up to the point where you said that which I have quoted above. Among other things, one thing which comes to mind is Jesus' words, “And when they persecute you in one town, flee to the next.” (Mt 10:23). I'm not suggesting that you necessarily consider moving to another town, but what I am suggesting is that (using the principle behind Jesus’ words) you consider moving on from your place of employment.
Assuming that everything you are saying is accurate, it seems you are not being supported very well either as a member of the congregation or as an employee. While I admire your dedication to your employer (often a rare find in today's workforce), it seems to me that there may be an over-expectation on the part of those in leadership at your church, if there is no one else who can fill in for you to the point that you are unable to take time off if needed. You cannot be held responsible for what sounds like poor management/leadership, assuming I am understanding the situation correctly.
Jesus expects us to die to our own self-will to the point of adopting a slave-like attitude toward service to others (willingly regarding others more highly than ourselves - Php 2:3). Willingly adopting a slave-like attitude for ourselves, however, is wholly different than having or allowing others treat us as slaves.
Put differently, there is no reason for you to feel bad or guilty for taking care of yourself (think good stewardship) in fundamentally healthy and God-honoring ways. If this man, Tom, truly is repeatedly behaving in sinful ways towards you (and it certainly sounds like he is, having heard only your side of the story and not knowing Tom, myself), I think it is safe to say, Jesus would not expect you to continue putting up with Tom’s sin (God desires mercy over sacrifice - his mercy reigns supreme in regard to your life, over expecting you to sacrificing your well-being and safety for the sake of some church work getting done) as well as the potential sin of the church leadership in not providing a safe working/worship/service environment for you - though in their defense, it sounds like they (unlike those of us here on the forum) know Tom and seem to see him as a good guy and my find your account of the situation hard to believe. Note, I am not suggesting you are lying. I’m simply saying that from their perspective (unlike those of us here), the whole situation is a “he said, she said” sort of thing. Though they seem to have sided with you on some level, that doesn’t mean Tom hasn’t put his own spin on the situation and they are stuck trying to determine, the best they can, what has really happened.
I highly encourage you to move on (trust me, others will figure out how to do your job without you if needed). If Tom is already following you and your sister both on social media, your moving on from your church may not be enough to keep him from continuing to pursue your attention (sorry to say). But staying where you are certainly isn’t going to help, while leaving, on the other hand, might.
You’re under no obligation to stay. I realize all of this is easy for us to say and difficult for you to do, but sometimes we have to do the hard things in life (and staying where you are isn’t going to make things any easier).
Whatever you decide, please be safe. Seek friends/relatives you trust to “always be around” for a time so you’re less likely to “bump into” Tom while out-and-about around town or outside of your home while you are alone.
You and Tom and your church leadership will be in my prayers. Hopefully, the church leadership will see reality for what it is and Tom will get the help he seems to need.
Blessings to you.