Seems to me that things got so bad so fast that Adama didn’t have time to try to get her in the loop. He let Helo and Tyrol go to Pegasus on the assumption they’d get a fair trial. From the time he learned they were going to be executed to the end of the episode is pretty much a straight shot.
If I were writing the show, I’d resolve the cliffhanger not with a Cylon attack, which is a literal deus ex machina and just postpones the actual conflict, but by having Laura Roslin just getting caught up with the facts of the situation and calling Cain directly:
“Admiral. Stand down.”
“Are you joking?”
“According to the Articles of Colonization I am your superior, and if you have any respect at all for the civilization you claim to be defending, you will stand down.”
“What possible leverage do you have?”
“Admiral, I’ve already dealt with one coup. Don’t underestimate me.”
Or something to that effect. If nothing else, learning that Adama staged a coup (if she missed that in the logs; you’d think she would have mentioned it in her little list of transgressions) would certainly intrigue Cain.
Or… Roslin could play the Earth card. I’m a little surprised that little tidbit wasn’t more important currency in the episode; as happy as Galactica’s crew is to see Pegasus, you’ve got to think the people of Pegasus would be equally or more happy that Galactica brings them a bona fide frakkin’ prophet who has fairly definitively revealed to them the location of the lost mythical homeworld.
In any event, it would be fascinating to turn the tables on Cain and watch her chafe under what she perceives as misguided leadership the same way Adama is. Until the inevitable conflict re-emerges, of course, in some form.
And whatever that is, I have faith that the resolution will not suck. It won’t be a dumb, obvious Star Trekky thing where the wayward officer rediscovers honor and sacrifices him or herself for the good of the fleet, or something equally dopey. Whatever it is, it’ll be cool.
You know how I know this? Because before this episode, we had looked at the preview, and we said to each other and ourselves, “Oh, no, it better not be a cliched story where the new officer and Adama clash and plunge into a power struggle.” And it wasn’t: It was an amazingly good story where the new officer and Adama clash and plunge into a power struggle.
This show just gets better and better.
I thought about this. There’s no reason he couldn’t have said to the head flunky, on the way in: “This is the carrot: Tell her what she wants to hear.” And they’d assume he was simply lying to her, and they’d grin at his shameless manipulations.
By the way, don’t overlook the rather significant little piece of plot information that got sneaked in among all the cross-character conflict: Cain’s description of the two Base Stars and the Mystery Whozit that have been following the fleet around. This, I think, is the only really viable escape from the plot trap they’ve built for themselves, the apparent choice between “the Cylons really are trying to kill them but they’re just inept” vs “the Cylons have a grand plan and our heroes are just chumps.” If things really are proceeding according to Cylon plan, the earlier our heroes learn about it, the earlier they can retake the advantage, try to figure out the plan, and monkey-wrench it. Cain’s small revelation might be the first step down that path; I guess we’ll find out when Starbuck gets back.
But yeah. Frak. Frakkity frak frak frak.
Now we know how the UKers felt for the few weeks after they first saw Boomer put two into Adama’s torso. 
I’m such a drooly fangirl…