My daugther is nearly 6 years old and my son just turned 2. How can I make my son stop hitting and biting and throwing things at my daughter? Should I let her deal with him on her own or step in?
For your first question, the best way to deal with your 2-year-old's behavior when he harms his older sister is probably to move him away and gently tell him that we don't hit/bite/kick/throw things, etc. Then move him to an alternative activity away from his sister. If you want, you could start trying time-outs with him (generally 1 minute for every year of age is the recommendation so he would get a 2 minute time out). I say this with a warning: I tend to think that most 2-year-olds don't really "get" the whole time out thing until they're closer to age 3ish and sometimes even later. So for the first little while whenever you put him in time out, you'll probably need to be prepared to sit with him in time out or be prepared to continuously send him back to time out because he'll get up. And he will probably continue attempting to attack his sister for awhile.
The root of the behavior is probably not malicious. He's probably angry because his language skills aren't sophisticated enough to express what he really wants to do and that's frustrating. You can help this some by encouraging his language skills and talking to him about feeling angry and sad and upset. For example, you might say, "I know you're angry because your sister is playing with the toy that you want to play with right now, but we do not hit people." Or something along those lines.
As for your elder child, it's probably a little outside the abilities for most 6-year-olds to deal with their younger sibling's behavior like this on their own on a regular basis. Instead, I would teach her (and I've been trying to teach my almost-6-year-old this as well...it's a process) that whenever her sibling harms her she needs to move away from him and go do something else. This helps to reinforce to her brother (even though he doesn't know it) that if he treats her badly then they can't play together or sit together or whatever. She can even say to him "I'm not going to sit with you anymore because you hit me".
The difficulty in this approach is that it can be hard for a 6-year-old to stop playing with something and move to another room or something. They don't see the benefit of moving themselves out of the situation--only that they have to stop playing with the toy. If you can get her to use this, though, it could mean that you don't always have to step in every time something happens. The consequence for hitting was immediate (your daughter went away) and your son no longer gets to interact with her for awhile.
As an aside, I have found that my daughter (my younger child who is 3 1/2) is much more physically aggressive with her brother than my son was in general (he will turn 6 in a month). He was NEVER a biter/hitter/kicker/etc., but she has been known to smack, hit, throw things, etc. I know this sounds crazy, but I think a lot of her frustration comes from the fact that she thinks that her brother is the best thing in the whole wide world and she doesn't always understand why he doesn't want to play with her ALL THE TIME. Or why his toys aren't always appropriate for her to play with. Or why he gets upset when he spends a lot of time building an elaborate Lego construction which she promptly tears apart. I just try to encourage him to be patient with her and to take a time out from her from time to time if he needs it (go to his room and play with toys there, read a book, play with the iPad, watch an episode of something on TV, etc.).