Eric Roberts (Thomson) let Meredith go because he realised that she was only a shoplifting chav living in a trailer park because she thought baby Claire had died in a fire, when in fact, Thomson, Sulu and the Company had given Claire to Noah. I forget exactly why they did that, maybe they thought Meredith had died instead. Anyway, Thomson was feeling remorseful.
Sylar killed Chandra Suresh to get his list of people with powers (which is presumably how he made his map that he was chucking away). He didn't just kill Chandra for the fun of it. I agree they're twisting the facts a bit here, but it's not totally inconceivable that Sylar would feel bad for killing people, but then go right back to it when the one person he trusted turned out to be a lying weirdo who brought round people for him to chop up.
I didn't Elle had been allowed out in the field this early, I'm sure they said she'd been in the Company facility most of her life (which was why she tortured Peter), but maybe I'm wrong. I suppose they'll say she turned evil because she got pissed off at the way the Company treated Sylar.