I agree with most of the other posts here that the best thing to do would probably be to stay somewhere else, but in case that’s really not financially or logistically possible, I’d like to add some ideas on how to talk about these things with her. I don’t think you want to confront her, because she sounds like she would quickly become defensive and angry. But, I also don’t think you want to join the “no” game. This is too stressful for your son, for you, and probably for your MIL too, so it’s not working for anyone.
I think you could try exploring parenting goals in a non-confrontational way. So, for example, during a downtime when the kids are sleeping, see if you can engage her in a conversation about how people parented when you and your parents were growing up, and maybe ask about when she was growing up. Share a memory you have, ask her about your childhood. Try to insert the idea that you or your parents were raised at a time when children were expected to learn how to not touch things, but now child development specialists think it’s more important for very young children to be able to safely explore their environment because that’s how they learn. You want to try to see if by acknowledging your own parenting learning curve, you can open her mind to other ideas. Then, when she tries to intervene with your son, which she probably still will, you can intervene and remind her that you are approaching this a little differently. You’re not trying to judge her, just reassure her that you’ll make sure nothing gets broken, and ask if there is something she is worried about. If she can tell you her worry then you can address it.
For example, my FIL was horrified at how frequently I was nursing my baby, and after a few rude comments he made, he finally asked “what does the doctor say about that”, which given his respect for doctors, allowed me to say “the doctor says it’s great to nurse on demand”, and reassure him. I asked him questions and learned that he had been told that bottle was best when my husband was an infant, and we chatted a bit about how things change every generation. He still asked me sometimes about it, but once we had that conversation, his comments got less rude, so I could more easily reassure him we were fine. When my kids got older, this strategy came in helpful regularly, engaging him and addressing his worry, but holding firm that my husband and I had a plan we were sticking too. It did get easier over time.
Be confident that you are doing what you know to be best. Also, remind her how grateful you are for her important role in your children’s life, for letting you stay with her, for all the toys she has given your son and try to find things that he likes to do together with her that are easy for her. Maybe thank her for reminding you of the importance of cleaning up after play, but since he’s so young, you will be the primary one cleaning up. If you're feeling tired and want to wait to clean up, tell her your plan, "I'm just going to let this sit for a little while, so I can take a rest with the kids, is that OK with you?" When you're up for it, try to beat her to the punch so she doesn’t yell at him, just let him know when you’re done with a toy, you can put it away and keep it fun. Gently intervene in a reassuring way if she tries to teach him the “right” way to play, by suggesting to her “let’s just watch and see what he does. It’s OK if he doesn’t know, he’s learning.” I would take a gentle, teaching approach with her, and see if she can calm down.
If she can’t, then I do think you either need to stay elsewhere or cut the visit short.