Much like with an order, there is no way to delete a marketplace, channel, or store from your account. However, you can make them inactive, which will essentially hide them from view within the app.
Head to your Account Settings (the wrench icon in the upper right).
Next, select Selling Channels and then Store Setup from the sidebar on the left.
Here, click on Edit for the store you wish to mark as inactive. Under the store's logo, you should find a checkbox next to Is Active? Simply uncheck this and click the Save Changes button.
This store, and all of its orders, will now be hidden from view.
As with any cancelled orders, inactive stores' data will not be included in any reporting. If you ever want to make a store active again, simply follow these instructions again, but check the box this time.