I agree that the main purpose of the excavator is pretty meaningless right now. Even without quarries, gathering metal or sulfur is significantly faster by hand. High quality metal is the only one that might be faster by excavator. Not only that, but it requires you to sit and stare off into space for an extended period while you wait for it to dig.
As for the scientists, i think it is a god awful idea to increase their health, in fact i think it needs to go in the opposite direction. AI in rust is broken, they are aimbots on legs with heads that can tank a shot from an l96. I'm all for a challenge in games, but they aren't a challenge, the only factor in whether you win or not is if you brought enough meds, because if a scientist sees you, you WILL need to heal.
Personally, i'd love to see a chinook come in every X minutes the excavator is running, to drop off more scientists and maybe even hackable crates. If a heli showed up carrying 4-7 scientists with 1-2 heavies as well, every 5-10 minutes that the excavator is running, it would keep it more entertaining, and bring some purpose to using the excavator.
As for the excavators rates, they'd need to be increased to an insane level to make it worth using. If i'm not mistaken, the excavator provides 400 sulfur per diesel. At level 1 mining skill, you get around 300 per node. There are a lot of areas on the map that you will find a node every time you turn around. At level 47 i get 440 sulfur per node. Running around smacking rocks, is also a lot less boring than standing watching an excavator swing back and forth.