Yes, it's a child-led room, but you still rule the house and are ultimately in charge of decisions. If there is ever something that you don't think is safe to you, your child or your property you can certainly adjust the situation. I have to set boundaries all the time with children and it never affects our relationship when done comfortably and confidently.
The first step is to make a decision. Decide what your boundary is and stick to it. Try to be as comfortable as possible. Remember you are setting the boundary to keep everyone safe and be confident in your decision (if you are not, your child will know and may button push.)
2. Explain the boundary to your child. ("It's ruining the markers when you chew them. Keep them out of your mouth or I will take them away.") The more straightforward the better so it's easier for your child to process.
3. Offer an alternative. ("Here, you can chew on this chew toy instead. Its safe for your teeth.")
If your child follows your suggestion celebrate him/her for cooperating to keep everyone safe and healthy!
4. If your child persists with the behavior, take the item away and put it high on the shelf until the end of your session. (If your child fights you trying to hold the item just hold the other side of the item and neutrally hold onto it until your child lets go.
Remain calm and consistent (make sure the whole team enforces the same boundaries) and it shouldn't take your child too long to remember the boundary.
Of course each scenario is different, if you have questions, please ask.