If it's a free game then you shouldn't be using a commercial engine. If you do use a commercial engine in a commercial setting then you need to make sure that you make a profit after you've payed your costs. This is not different from any other type of commercial enterprise.

If you are going to go with an ad based model for your game, like you suggest, then you should be able to make a profit if enough people use your game, which should be somewhat proportional to the amount of installs. People aren't just going to install your product and never use it. What could happen of course is that they use it once or twice and determine it's total crap and then don't spend any time actually playing it, so not enough ads can be displayed. In that case you should indeed delist the game, because it isn't viable. This should be easy to track based on the number of downloads and ads revenue. But of course if your game is crap then you can also expect people to not download it in the first place, so it isn't a very realistic scenario. If your game is slowly becoming more popular, like you suggest, then you should be able to make enough of of it to pay your dues.

Perhaps what could happen is that you manage to stir up an incredible amount of hype around your game. A ton of people download it and then simultaneously determine it is crap without listening to game reviews and such. However, in this case I can hardly imagine that the business model was ad based revenue when you've got the marketing budget to stir up such a hype.

Nevertheless I wouldn't say it is completely out of the realm of possibility to get cornered by Unity's business model, or any third party business model as of fact, but it's unlikely if you think it through. And that is actually part of the risk of entrepreneurship that you need manage. A friend of mine also had a clothing store and bought a bunch of clothes that in the end she couldn't sell and needed to default on her payments. It happens. The clothing store industry is much harder than the game industry: you need to buy everything up front and then hope that you're going to be able to sell it.

Unless you're dealing with a liberal open-source license, you can't just expect to go out into the world and use somebody else's work without having to deal with these types of issues. And that is just fair, if you'd ask me.