It's ridiculous to charge for this. But there's a fairly easy solution, although it will be a bit of a hassle at check out.

Just remove enough items so that your water bottles fit. Set them on a table, desk, wherever. On your last day, replace the items, take a picture of the full fridge and stop by the front desk to dispute the charge. They may go to the room to check, so this is why it could be a little annoying. But I've never encountered a problem having a false charge removed for a minibar if all the items are still accounted for.

No need to take the items to the front desk, ask for another refrigerator, ice buckets, or any of the other complicated solutions. I always find it better to go with the easy answer and not ruin my trip by having to prove my point in some dramatic way.