If a SOI graduate is assigned to a unit that is currently deployed, will that graduate get sent to join the unit or wait at the home base for the unit's return? I should mention that the unit in question was deployed over 6 months ago but their stay has been extended for an additional three months.

Most units maintain a rear presence back in the states. Very likely he'll be assigned there first. Once there, it may be determined that he can receive orders to join the main body as a replacement due to attrition.
I know that doesn't relieve your worries about what is in store for your son. Rest assured that if and when he does deploy, his command has many combat veterans that will take him under thier wing and show him the ropes. They don't just turn them loose and hope he learns on his own.

Thanks for your logical explanation and kind words about Marine "on the job" training. I am beginning to understand how Marines take care of each other and it's very encouraging to me sitting here at home.

The guy's in his command will watch out for him. Pretty soon he'll be doing the same for the new guy's checking in. We all went through this and is part of the learning experience.

It used to be the Corps had a severe shortage of active duty combat veterans, but not anymore. The Commandant recently issued the instruction that all Marines will be rotated through the area of operations to ensure the Corps gives all Marines the experience.

Your son just went through the most comprehensive combat oriented training the Corps has ever developed. When I was in, our combat training was just the basic stuff from boot camp, and then we'd get orders and step off the plane or ship and move into the area of operations fresh from boot camp. There we would learn the ropes from those that had been there longer. Back then one was the FNG (frigging new guy) until another FNG showed up and then he was it.