I'm not entirely sure how many times the dissidents had done this, but certainly they did seem to know what to do. I'm sure they have to avoid doing it too many times, because they can't have every ship coincidentally getting bombed in orbit of Prime.
You're very right: had Dukat not had a daughter, he probably would have backed out. I'm not 100% sure how his judgment would've been since he's off his meds at this point. (That said, without Ziyal, he probably would've attempted suicide again after the rape.
He does care about the woman in the slave camp, though, and I know he wants her to be rescued. He meant the angry things he said to the dissidents--that they should have at least ensured the pilot's wife was out of the camp and recuperating somewhere safer.
I suspect that at some point Dukat will regret snapping at the pilot to shut up about Ziyal, but with all the emotional turmoil he's going through and that he's about to face--and the fact that he is off his meds--my guess is it will take him some time to process that. AU Dukat is not a man who holds a grudge anywhere near as easily as Gul Dukat, but I know that an insult to family is the hardest thing for him to let go of.
I think that the pilot began to realize how Dukat cared for his daughter. How hard it was for Dukat to have to carry her drugged unconscious for the entire flight so that earlier in the flight she didn't give away their presence to the Bajoran crew or knock her mask off and take up oxygen they couldn't afford in there. Maybe the pilot wondered how he would've handled the situation in Dukat's shoes if he had been trying to get a child off of Bajor.
At least Dukat is "in his element" now, back in the desert. But if you read "The Guide," you'll see what happens after that.