Unfortunately, I don't know a good way to really do that, either under the current or the upcoming system. You have to practice skills to increase them, with very few exceptions like meditation and perception. Part of what first got me into starting combat with Alia in fact.
That said, one possibility might be not training her defense so much as training her stealth. Perhaps she doesn't like to fight, but she can be a sneaky git if she has to get past hostiles to get to a patient. Not a perfect solution but it's a thought. Alternatively, just plan on having a guard in a situation like that. I know you did that at least once before and it worked pretty well.
Going back to skill things, I haven't been keeping up on this thread but I've definitely found myself at times wishing it was already in, ha! Mostly it's when I've spent all of my skill points, have 12k to level and I'm about to spend hours doing some other thing and wishing I'd get at least a little skill increase for all that. I really am looking forward to it, though I know there's likely going to be parts about it I grumble about. A game can't be perfect for everyone, after all.