These two novels, by Judith Proctor (aka watervole), are:
Price to Pay
Truth and Consequences
Here's the author's own summary of Price to Pay: When four-year-old Sunlight on Water came through the Stargate looking for her father, Jack O'Neil's problems were just beginning. Explaining how he came to have a daughter was only the start, dealing with her symbiote was a total headache, and as for the letter that she brought with her...
When I read that, I thought it might be the sort of story I would prefer to avoid. However, the further into it I got, the more involved and intelligent the plot and the treatment of the characters (especially O'Neill, and Maybourne) got, and the more wrapped up in the story I became.
I don't want to spoil too much, but there is some lovely Tok'ra stuff, character angst that is *earned* by the plot (which is how it should be, imho), tangled webs of personal feelings vs. military orders, and something that I've never seen a fic author get away with this cleanly before: take someone as cheerfully amoral as Maybourne through such a wringer that when he turns around and reaches out for God, it's not only stunning, but I actually completely believed it. Not the only stunning moment in these fics, not by a long shot, but maybe the one that surprised me most.
Anyway, if you like SG-1 and are interested in reading a solidly plotted, character-accurate, detailed sort of AU...this is what you want to be reading.
What are you waiting for?