I understand how you feel. You'll need to have a discussion w/your MIL and tell her that you appreciate her picking up your son and spending time w/him at your house, but you would prefer she not do anything to your computer and be careful about not letting the cat go outside. Set some "gentle" boundaries w/her because she truly doesn't know where she fits in w/the family now that her son has gone AWOL.
You've had quite the week and it's not over yet...but you'll feel better when the weekend comes. Dealing w/MLCers and families are difficult most of the time, but when they "invade" your space it gets old very quickly.