Am I supposed to continue trying to help this lady? I know many here do not believe in God anymore, but what is His will in this situation?
I'm not really the person to be answering your question, as I don't believe in the Bible God. The composite texts known as the Bible make it very clear that the being who is described there is a philosophical concept that changes over time. That being said, if God does exist, and wants you to help these people, how would he make it clear without communicating clearly? How can you distinguish what is happening from coincidence?
I've seen people make so many bad decisions due to magical thinking ("If I pray for something and it happens, it must be from God so I should follow this course" -- later, "Maybe this wasn't such a good idea"). I think it's best to stick to what you personally feel is the right and compassionate and practical thing to do. It's good that you want to help them, but if you are coming to the conclusion that you might as well be talking to a wall, then you should give yourself back that free time that you would be wasting on her.
Should I run and protect myself from her?
I don't think you have anything to fear from her. You don't think that there's some secret backroom course in mind control that Witnesses take when they become "adepts", right? They're just sadly deluded people who want to spread their mind virus.
Why does she keep coming back here?
To prove herself righteous, or get her hours in, or both.
After making declarations that I "just don't have time to deal with this," I started getting these nagging reminders in my mind that it is not for me to always understand the purpose of the trials and challenges in my life.
More magical thinking. Didn't Jesus say that time and unforeseen occurrence befall us all? Didn't Solomon express that the swift don't always win the race? Things happen. How can we claim to know whether there is intent behind them or not?
Will the decision to quit meeting with her, mark me in some way? Will the JW's stop calling on me, or will even more of them start avoiding me when they see me in public?
Nope, not at all, unless you do something to get labeled an "apostate". I know you've made it clear to some JWs that you have viewed apostate material, but you haven't pushed it on them, so they simply view you as a poor "stumbled one" who needs help getting free of apostate lies.
Do the different congregations communicate with each other and compare notes?
No, but who knows if she personally knows someone in another congregation that knows you? At least, I don't know.
So they will keep coming back, no matter what I say?
Not at all. Hand her something "apostate" (make sure to tell her what it is, since she won't read it) and you'll probably never see her again.
Are the service hours their main focus?
If you were being held to a yearly quota and made to feel ashamed if you fell short, you'd be desperate too.
Will what I say to one, stop another from coming to the door?
Does shooing a fly out of your house stop other flies from coming in? You're imputing way too much organization to the organization. There are do-not-call records, but they're not well-maintained and often ignored by the publishers when going door to door. There's also some pressure not to put people down on the DNC list even when they explicitly ask to be.