"In the college life of Barack Obama in 1961 and 1962, as recounted by his friends and acquaintances in Honolulu, there was no Ann; there was no baby."

Writes David Maraniss, at page 171 of "Barack Obama."

In Neil Abercrombie’s crowd, the antiestablishment group that carried on a movable conversation from the Snack Bar on campus to George’s Inn and Peter Gilpin’s apartment, only Abercrombie himself could dredge up memories of Ann Dunham in 1960. By the following year, the year he was married and had a hapa son, Obama had developed another large network of friends and acquaintances on campus....

Here's what Abercrombie remembered (pp. 157-158):

These gatherings, they weren’t necessarily formal, but we would see each other and all that. She made her appearance, but she was a girl. And what I mean by that is she was only eighteen [still seventeen, in fact, until November 29]. She had just got out of high school the year before, she was a freshman, and he met her and he brought her at different times.… She mostly observed because she was a kid, among other things. Everybody there was pretty high-powered grad student types, and the women were older. She never participated much in the discussions, but she was obviously interested and obviously interested in Barack. He always saw himself in charge of everything. And don’t forget he was also very much a man of his time. We’re talking the nineteen-fifties culture and we are just beginning to talk about patriarchy, just beginning to try to figure out what feminism is all about, just beginning. In the Beat era women were still seen as servicing men. They hadn’t gotten past that, or even in remotely understanding that dynamic. The whole Kerouac era when you read it now is almost misogynistic. As Thoreau said, you drag your cultural baggage through life with you. In any event, Barack, I expect he dominated the relationship is what I’m trying to say.

As Maraniss puts it, Dunham and Obama Sr.'s "time... together" was "a brief point of confluence with few witnesses or supporting documents." They did marry, after she became pregnant, but he already had another wife, and they don't seem to have lived together.  A friend from that period described Obama Sr.'s apartment:

“I could see no sign of other inhabitants,” [Robert] Ruenitz said. “It was monastic at best. A study table and a bed and a light. It was not a dorm. It was private. I think he had a landlord who had built a small attachment to their house. It was small, and I think he had a hot plate for coffee; not very well appointed. It was not close [to campus], but I think each day he would walk to school.”

Maraniss says — at pages 175-176 — that apartment "reflected the reality of a man who was married in name only."

Within a month of the day Barry came home from the hospital, he and his mother were long gone from Honolulu, back on the mainland, returned to the more familiar turf of Mercer Island and Seattle and the campus of the University of Washington. The question of why they left is what lingers, unresolved. This period, Washington State revisited, is missing from the memoir the son would write decades later. In his account, the family breach would not occur until 1963, when his father left the island. That version of events is inaccurate in two ways. The date: his father was gone from Hawaii by June 1962, less than a year after Barry was born, not 1963. And the order: it was his mother who left Hawaii first, a year earlier than his father. 

Maraniss surmises that Dunham left because of the apparent bigamy. He notes that there might have been physical abuse, though the only evidence is Obama Sr.'s abuse of his next wife. He doesn't mention what would seem to me to be the easiest explanation: That Obama Sr. married Stanley Ann Dunham only to make the baby "legitimate," and there was never a prospect of living together as a family. That fits the facts, including the fact that Dunham didn't want to talk about any of the details.

ADDED: There is a subsequent letter written by Obama Sr. that refers to "my wife" — not "my former wife — "in Nairobi" (p. 180). This letter makes no mention of the additional wife, Stanley Ann.