The writing has set up a precedent that yes, some things are slightly different in the Flash Sideways, but the relationshps are consistent.
Locke and Helen are together as they were in the original timeline. Same goes for for Rose and Bernard and Sun and Jin.
Likewise, they've shown that family relationships are the same. Jack's mother is the same woman. Locke's father is still Anthony Cooper (or so we can assume, given the pictures in his cubicle). Shannon and Boone are still brother/sister. Claire is somehow (we have to assume she's still Christian's daughter, but we don't know for sure) involved with the Shephard family.
To me, it's reasonable to assume that Jack STILL married Sarah at some point in the Flash Sideways because the family/spousal relationships have been the same. They may have met differently or divorced for different reasons from the original story, but I believe they still would have had to have met and gotten married.
The Flash Sideways is tricky because we know there ARE differences, but the majority of things are the same. Jack is still a doctor. Locke still worked at a box company and is paralyzed. Kate is still a fugitive. Boone still went to Australia to get Shannon to come back with him. Rose still has cancer.
So, I don't see something as drastic as Jack marrying and divorcing Juliet in the Flash Sideways happening because it's TOO different from what we know. Plus, can you think of a reason they would get divorced if they had married? They seemed to get along very well and liked each other a lot in Season 3. As much as a Sawyer/Juliet fan as I am, I can't wrap my brain around a reason why Jack and Juliet would divorce if they had gotten married unless both of them being too pretty and too successful are reasons. :) It just doesn't make sense. I guess you could say that like On-Island!Juliet, FlashSideways!Juliet could divorce Jack because she realized that he doesn't really love her, but that still doesn't make much sense because the reason On-Island!Jack didn't love On-Island!Juliet was because he REALLY loved On-Island!Kate, who he has only bumped into in the FlashSideways. So, you can't make that same case for their divorce.
I was thinking about how the story has made a big deal of variables and constants. If things change, part of me thinks that those come into play. The Flash Sideways reality has both constants and variables. For me, David is the variable in that reality...so, there has to be a constant (Sarah) associated with him. To me, it's too much to believe that there were be two variables (David and Juliet) in Jack's past like that...if that makes any sense.
In the Season 2 episode, "The Hunting Party", Sarah tells Jack that she took a pregnancy test, but it was negative. Could it be that in the Flash Sideways reality, the thing that changes, the thing that is different...the variable from the original timeline is that this time, it's positive? I totally believe that.
Sarah was pregnant in the Season 3 finale, so in some weird way that I can't fully explain, it would be a nice tie-in to her having a baby in the other reality. Of course, this segment of my entry is a weak argument because Juliet Bowen, truly, was pregnant in real life during the shooting of that finale, so they just used it. I don't think it was actually driven by the story. But, STILL...they could use it.
Juliet did have baby-making foreshadowing in Season 5 (see her conversation with Amy in "Namaste"), but that was in relation to SAWYER, not Jack. Could they twist it around? Sure. Do I think that makes a lot of sense? Nope. If it had been..."So when are YOU (just Juliet) going to have one of these [baby]?", that would make sense for a Jacket kid because it's open-ended. However, it was specifically, geared to a Suliet baby (James was mentioned), so I don't think it makes a lick of sense for it to, randomly, be a Jack/Juliet baby.
The Enhanced versions of the Season 6 episodes have said that the FlashSideways world is showing what life would be like if Oceanic 815 had never crashed. If that's the case, then it seems to reason that whether or not the plane crashes has no effect on the past because it only changes the future. What does that mean for David's existence? I don't know. But, I suppose you could argue that in a world where Oceanic 815 never crashes, Sarah and Jack could have had a kid just as much as you could that Jack and Juliet could have met somewhere else (Med School? Hospital where they both work?) and got married, had a child, and got divorced.
Before I get into more extensive thinking (for me, anyway), I should say that this might also be a time to apply
Occam's Razor. Instead of trying to figure out who ELSE might be the mother, maybe it's better for us to think who would be the mother, based on the past information we already know because that could be the simplest solution? I know it's LOST and they're all about twists (and we love them for it), but it's also a show that does a great job of setting things up and paying them off. They understand precedents and formulas. They understand that they have to make things make sense and do a fairly group job at doing so (to me, anyway...others may disagree).
I was thinking about Crisis on Infinite Earths...and how there are parallel worlds: Earth-1 and Earth-2. In both worlds, Superman and Lois Lane are together, but it's their lives/cirumstances that are different within them. They're romantically involved in both worlds, but on Earth-1, they work at The Daily Planet and on Earth-2, they work at The Daily Star.
So, to me, it makes sense, with that analogy, that since Earth-1 Jack and Earth-1 Sarah got married and divorced, same would happen to Earth-2 Jack and Sarah, but their Daily Star (their variable) being their son, David...if that makes any sense.
All the relationships that were formed because of the plane crash or after the plane crash have now formed after the plane landed. Ben and Locke met post-crash on The Island and now, in the Sideways world, after the plane lands. Same for Hurley and Locke. Boone and Locke. Jack and Locke. Jack and Sayid and Jack and Charlie and Jack and Rose. Rose and Locke. Jack and Kate and Sawyer and Kate and Kate and Claire. None of those relationships formed PRIOR to the plane landing in the FlashSideways (except, okay, maybe Rose and Hurley, but I don't know that we know they know each other, personally...she just happened to be the person who worked at the Temp Agency; Hurley may have just referred Locke to the office, not specifically, to Rose), nor in the original timeline, but with the plane crashing on The Island. So, it makes NO SENSE to me that, randomly, Juliet and Jack would have been married before the plane landed if they only met post-crash in the original timeline because the only ones who are together BEFORE the plane lands are ones who were originally together in the original timeline.
I can understand the speculation that Juliet is the mother, given that Juliet was, originally, a divorcee' (divorced from Edmund Burke) and has blue eyes like David, but given what the show has set up, I don't see it happening. It makes MORE sense to me that it would be Sarah than Juliet. I'm not totally discounting Juliet, but I think it's more likely to be Sarah...for lots of reasons.