When you disable a channel in EffectConnect, you basically stop the updates and synchronization, but this won't empty your seller account so everything in your seller dashboard will remain the same. It just won't get updated anymore.
To remove all the products from the marketplace, the best you can do is manually delete all the products from your seller account. If this isn't possible, or you need a bulk delete of your products, you can contact your account manager or seller support at the marketplace.
You can however avoid unwanted sales by first configuring a stock margin in EffectConnect. For example a margin of 9999 pieces. In this way, all your products will be set to stock 0 and not get sold anymore. You can configure a stock margin when configuring your channel.
Please keep in mind that, after setting a stock margin, it can take a while before the stock is updated on the marketplace. To read more about the synchronization times, read this article.