the first question has been asked about 50+ times on this site. I'm not going to spend time answering it.
As far as Squatting and deadlifting, why in the heck wouldn't you want to do these?
You're not going to get very strong by only doing arm care stuff. Keeping your arm healthy doesn't just mean keeping the rotator cuff, elbow flexors, etc. in shape.
It means getting THE ENTIRE BODY in shape.
Paul always says and I agree, 97%+ of those who complain of injury or arm pain HAVE NOT CONDITIONED THEMSELVES TO THROW THE BASEBALL. You should spend at least as much time preparing to throw as you do actually throwing. How many can honestly say they've done that?
It is my belief (and there is considerable evidence for this, check t-nation.com or ask KC) that one of the primary goals of any conditioning program is to improve rate of force development (as well as helping to thicken/strengthen the body's tendons/ligaments/connective tissues). That being said, some of the most important lifts you can do are the ones that RECRUIT as many muscles as possible. This is called neural recruitment, and is the idea behind weighted ball training as well. Being explosive and lifting HEAVY weight are two ways to improve RFD.
Why would you avoid Squats and Deadlifts? Are you afraid of injury? They are safe once you learn correct technique (it take all of 5 minutes to watch a youtube vid). And for reasons I've already stated they will be SAFER in the long run because they will help your body to stay injury free by strengthening connective tissue, etc.
If you havent done your homework, Centerfield's log is a good place to start. Poke around t-nation.com too if you're curious. Hope this helps, just my rant for the day,