Hello Mrs Dalloway, I believe you are right. Maybe the husband decided to go back to sea, which is why Dawn's character has ended up in prison again, and sent the baby to Alf? Presumably the husband was unable to take care of Patience, either because he was back at sea, or because he was unwilling to do so.
It's just another of those Larkrise quirks, which makes the series so intriguing and keeps us hooked!
On a different note, has anyone notice the lack of children in Candleford?