You have an advantage in that Hanna is already your friend. Wouldn't it be simplest to sit down with her one-on-one and talk about what you both want? It's not fair to expect someone in the middle to both perfectly understand your wishes (without knowing the right questions to ask) and then perfectly explain them to someone (without knowing the answers to the questions that person asks).
As for time distribution, don't forget that they are married and have a life together, a house and finances, all that jazz. I totally get that it sucks to be stuck at home with your husband overseas (mine works out of town, so I have an inkling, but I can't even begin to imagine going months at a time without seeing him) ... but try to remember, that's not Hanna's fault. She shouldn't be expected to give up half her time with her own husband just because you're dating him and yours is overseas.
I don't understand what she means by she's going to back away and not try to get time with Isaac. To me, that sounds like a guilt trip. I mean, they live together... of course they're going to have time together. Where is she going to go away to? Is she going to start living with her parents or something, and wait for Isaac to come rescue her?
It sounds like she's having trouble dealing with jealousy issues. It really does sound like she's trying, giving you guys space and time, but that she's struggling. She may be repressing feelings because she doesn't want to stand in your way, but that those feelings are brewing inside her and coming out toxic. Hence, the self-sacrificing guilt trips.
Finally, regarding alone time, I think you need to work that out somewhere other than her house. Frankly m'dear, it's not her problem. In her mind, she's already making a leap by sharing her husband with you and giving up time that used to be all theirs for you to see him. What about getting your sitter to take the kids to their house and having Isaac over? If that isn't possible, then find somewhere else to go together. In other words, if you want alone time with him, it's up to you to figure out how to do that, not up to her to leave her own house to give you that.
“As I am sure any cat owner will be able to tell you,
someone else putting you in a box is entirely different
from getting into a box yourself.” —bisexualbaker