That would be far too soap-operay. I hope not but it makes sense
From what I saw in the episode, it was a reaction. Anders was like "OH SHI-" and couldn't hit. Instead of Adama's old girlfriend he couldn't shoot as his gun was jammed, so he instinctively gave the signal that he was friendly don't fire. So the Cylons put two and two together and figured they should pull back for now.
Athena's been thru alot more stuff. She's been there for what 3 years now? Doing stuff like getting the keys for the engines of every ship to get their collective butts off New Caprica has to pay dividends. The Six unit screwed Baltar out of the codes for the Colonies defences(imagine what'd happen if they knew that?), and only got the baby back. There's still alot of work for here to be allowed free movement and even then she hasn't shown interest in helping the humans, only in protecting Hera.
On that note you got to feel bad about Boomer. All she did was get turned on and shoot Adama, now she's the demon stuck on the Basestars. She doesn't even have the option of redemption.
I'm thinking the last Cylon's on Earth now and will be revealed when they arrive.