C.T.
I think you need to address your MIL's actions/reactions to your child as they occur. And, I think you need to be sure to pick your battles too.
At the restuarant, I support you in your desire to keep him in his highchair. This is correct and safest in this environment and also leads to teaching good manners. I think you did good to remove him and calm him down, but, I think you needed to say something to your MIL like...
"I'd appreciate your support in teaching Son, that a highchair is the correct place for him to sit in at a restuarant. Worrying about his reaction will not assist me. Would you like to sit next to him? When he tries to get up, I would appreciate it if you would correct him and ask him to sit back down."
I think something along these lines during the other situations (even at home), would be helpful. Practice it a few times and have it ready to go. Be sure to state what your goals for your son are and how she could help support his development and the reinforcement of your rules, etc.
Good luck. This could be hard for a while.
~C.