My thoughts on the Martha thing:
1. Clark overhears Bruce at the Lex party. He knows he's doing something funny, so he researches him and gets his backstory...including Martha and Thomas' death. But he doesn't know Bruce is Batman...
2. He stops Bats in the "do you bleed?" scene and x-rays his face and discovers it's Bruce, the man he's suspicious about....due to his research, he knows Bruce's history, he has sympathy and let's him off with a warning....intending that to be the end. In other words, Supes has already changed his mind on Bats and decided he's alright enough to earn a second chance.
2. Lex kidnaps Martha. Says "kill the Bat". He knows Bats has the K-rock. Figures it'll lead to Supes' death.
4. Supes sees Lois and is upset cause he sees no way out....Flys to Bats...Tries to reason with Bats...fails and gets caught up in the fight/survival.
5. When down, Supes, knowing Bruce's history, INTENTIONALLY says "Martha" because he knows Bruce is thinking about his parents and they are important to him. He understands Bruce's vulnerability, and uses it against him. He knows how he'd react if he was Bats, and plays that to sway Bats' opinion of him.