Here's a place to post ideas/comments. I'll post mine:
First, remember that the greatest challenge for most aspiring thru-hikers isn't the physical aspect, but the mental one.
When you hike with a partner it's good to come up with a plan on what to do under a variety of conditions. However, doing that is probably as much fun as a prenup.

This is especially true if you want to continue going without the partner. Some romantic partners will decode your "abandoning" them as a lack of loyalty.
But it's fair to argue this:
a) If you're over 80% done with the thru-hike, then you can keep going without the injured partner.
b) If you've only done 20% of the trail when one quits, then you will both quit.
c) The remaining 21-79% zone is up to you to decide as a team.
The problem with (b) is that many people make enormous sacrifices for a thru-hike. Many hikers do what we did: sell belongings, move out of our home, and quit our jobs. So it sucks to make so much sacrifice and then have to quit just because your romantic hiking partner is getting annoyed with the mosquitoes.
Therefore, if you're going to make major changes in your life to thru-hike, then your partner must understand and appreciate that. Then she'll be more likely to understand your desire to go on even after she bails. But don't be surprised if the sympathy still isn't there.
Furthermore, it's hard to predict how you will feel. I read a journal of someone who kept going after his partner dropped out. Just a week later, that hiker also quit. The same might happen to you. Or if you get hurt, perhaps your partner won't quit and will get summit fever and to push to the end.
Two more pieces of advice:
1) Learn From Trail Lore. Both you and your partner should read books on AT (like mine!) as well as others. Read online journals. The more you understand what you're getting into, the better. However, realize that no matter how much you read, there's nothing like the real thing. Which brings me to....
2) Simulate thru-hiking over long weekends. Although many couples hike together, few backpack at a thru-hiker pace. When the weekend forecast was a rainstorm, Lisa and I headed for the trails to do 20 miles a day on Sat and 20 miles on Sun. We got wet and it was challenging, but we learned what it's like to backpack in such conditions. That training helped us deal with four days of nonstop rain in Maine and Georgia. If you can't deal with challenging conditions, the hike will be miserable.
If anyone has any thoughts on this topic, feel free to register and post!

- Francis