It's established that part of the networked computers includes the automatic landing system that guides Vipers and Raptors into the landing bay, that means there is an external access point.
Galactica was crewed by Adama's people, it's established that Adama has a soft spot for discipline cases and likes to turn people's careers around. Maybe they aren't the dregs but they also aren't a Star Trek style "god crew" (a lot of what Galactica is about is washing the taste of Star Trek out of Moore's mouth, Moore used to work on Star Trek and there was a lot of it that he hated, one of the things he has complained about is how Star Trek crews are always nothing but A+ the absolute best star fleet has to offer, no member of an Enterprise crew (of Voyager or DS9) was ever just good at their job). And Apollo hates being in the military and was planning on quitting when his current enlistment was up.
It's established shortly after we meet Caine that she has changed, she's more hard edged than Adama knew her to be. Just like how Col Kurtz wasn't always like we see him in Apocalypse Now Caine wasn't always how we see her in BSG. Different people react to extreme tragedies differently, Caine apparently snapped.
Okay, so the automatic landing system is an issue - isolate it from the main network (might be hard if needs input from Nav, but there are ways) and look for the next issue. Or limit its ability to accept input (do something about that buffer overflow trick... who wrote these things - Microsoft?). Or turn it off during periods of Cylon contact (have to park or land manually during battles). They need those systems.
The rest I agree with. But Caine is a babe... and I'd want to be on her crew (as of Pegasus, anyway).
Heh! I entered this quote in IMDB. It's one of my favorites:
Act of Contrition (#1.4)
Dr. Cottle - "You are obviously an intelligent well-educated young woman. Would you mind explaining to me why you waited five years in between breast exams?"
President Roslin - "Yes, I would mind. It's none of your business. I was busy."
Dr. Cottle - "[lighting a cigarette] And now here we are."
President Roslin - "Yes, here we are. Do you mind?[Indicating her displeasure at his smoking]"
Dr. Cottle - "I do, actually. [continues smoking]"
Doc Cottle's great!