Minecraft – Host bukkit server with regular server

In my opinion, your best bet here is to use Essentials' GroupManager. It's simple to set up, gives OPs all available commands and lets normal users play with basic permissions. All you have to do is download the Essentials Suite from here, paste the Jar files into your plugins directory and start the server to let it generate the default files.

Then, open plugins/GroupManager/Worlds/World/Groups.yml with your favourite text editor and tweak it a little. By default, new players will be added to the default group, which has no building permissions. If you change build: false to build: true under the info section, they'll be able to place and destroy blocks, and use a very basic set of commands.

groups:
  Default:
    default: true
    permissions:
    - essentials.help
    - essentials.helpop
    - essentials.list
    - essentials.motd
    - essentials.rules
    - essentials.spawn
    inheritance: []
    info:
      prefix: '&e'
      build: false
      suffix: ''

  ...

If you want to give your users some more freedom, change default: false to default: true for the Builder group. You can also remove some commands you don't want them to have while still conserving the other ones, such as essentials.kit and essentials.kit.tools. You can also change the group of the already existing users editing plugins/GroupManager/Worlds/World/Users.yml.

For more advanced Permission management, I'd recommend Permissions 3.x before DefaultCommands.

Edit: Here's a really useful command reference for GroupManager: forums.fragnet.net/minecraft/588-essentials-command-reference.html

Your config seems to be a little off. Get the latest version of bukkit and then select the option for structures: true. That should fix.