The more I think about it the more I realize that Carmen was in a no-win scenario.
Assuming that Carmen did love Howlett and Logan then she didn't have any choice but to leave the way she did when she was told by her superiors that she was to leave Sandrock.
This is also assuming that Carmen was a member of the Sky Sharks or rather was a member of the Everglade family. If that Sky Sharks post for Evershine was anything to go by it's that the Everglades have the very distinctive family traits of white hair and blue eyes. So Carmen wasn't just some random soldier turned spy, she was someone important because her family basically runs its own branch of the Duvos air force. So if she did go AWOL it would have been a high priority to get the traitorous Everglade girl back.
If Carmen chose to ignore her orders and stay, Duvos would have immediately tracked her and her family down. She would be branded a traitor and her family, or all of Sandrock, would have suffered for it. If she told Howlett (and going by what happened in ‘hot chocolate’ he would have forgiven her for being a spy) his answer would be to A. Stay and fight whoever came for Carmen, or B. Go on the run with Carmen and Logan. But going on the lamb with a four year old in tow would have been a recipe for failure. And Howlett, bless his soul, wouldn't want to endanger his town. Nevermind that Sandrock back in those days would not be prepared for an attack. If Carmen chose to go on the run by herself it still would have led Duvos back to Sandrock and to her family to use as hostages.
If Carmen went to Atara and formally betrayed Duvos to defect to the Free Cities there would be a very high likelihood that other deep cover Duvos spies would interfere and capture her or her family.
The only option she had that guaranteed Howlett's and Logan's safety was to disappear the way she did and go back to Duvos/her family. Even if her superiors knew that she had a husband and a kid in Sandrock as long as they were just a part of Carmen's cover and didn't interfere with her mission they likely wouldn't care about Howlett or Logan.
This family is so tragic. Even after all of that Howlett is still killed by a spy and Sandrock is still invaded. If Carmen chose to return to Sandrock now she would find out that Howlett is dead and Logan probably hates her just for being a spy let alone how she abandoned him and Howlett.
*nodding emphatically to all of this* Absolutely absolutely! I think the only option you didn't explore was Carmen bringing Howlett and Logan with her back to Duvos. Venti from My Time at Sandrock is from Baja, which at the time of MTAS is part of Duvos, so we know that people moving across the border isn't a huge deal, at least in peacetime. I think it's very possible she could have sat down, explained, and said, "come with me," and Howlett very well might have gone.
But. That would mean Logan would grow up in Duvos. The picture we have of the Empire is pretty bleak, and he certainly would've been dragged into service, especially with his family connections. A life on the run is no place for a 4yo, but growing up in a country with food production and resource issues that's constantly getting into wars with its neighbors really isn't great, either.
I can very much see Carmen doing that math and deciding the best answer was to remove herself from the equation. Let Logan grow up surrounded by a tight community with a pa that loves him, rather than drag her family into an authoritarian nightmare with her.
The most tragic thing, for me, is picturing Carmen as a woman genuinely trying to do her best. Like when I first hit that quest, I was ready to label her a deadbeat mom and toss her out with the bathwater. But what would have to be true for what she did to make sense? What if that really was the best option available? How bad was her situation for her to assess her options and decide that her family was better off never seeing her again?
... I have maybe written 56k words about it
