Each account has a setting for the default way to delete messages. The initial setting is “move to deleted first, delete from server when purging the deleted folder”.

To change the default: Go to Settings > Manage Accounts > Select your account > Options > Account Options > Deleting messages > Select "Hide in the app, keep on the server"

This will change the default action icon for deleting messages from this account to “hide”. Hidden messages can be restored by using the menu in the message list view.

Note: It is not really necessary to delete messages from the app — old messages are automatically removed over time without affecting the server, keeping storage usage under control. Aqua Mail by default keeps the 250 most recent messages per folder (this can be changed in each account’s Folders and Options as “messages to cache”).