The conversation between Kyoko and Sayaka in the church strongly implies that Kyoko does in fact steal the apples and that she knows that it's wrong.
The dead give-away for this is towards the end of the conversation. (ep 7, roughly 13:45 including OP)
- Sayaka asks Kyoko where she got the apples. Where she got the money from.
- Kyoko looks down at the apple and flinches. She does not answer.
- Kyoko then lashes out at Sayaka in apparent defense of her actions.
That's exactly the kind of reaction someone would get when they are caught doing something
In short, episode 7 paints a dark picture of Kyoko and her past. She's basically in "survival mode". So even though she knows that stealing is wrong, she still needs to eat. Without money or any other support, her only option is to steal and make the most of what she has. This is also why she gets angry at Sayaka when Sayaka throws the apple on the ground calling it a "waste".