By Default magento will only allow you to change this config option for the whole setup, you can't change it on a by store basis.
You can possibly update magento to allow you to specify different settings for this option per website to allow you to do what you need:
app/code/core/Mage/Core/etc/system.xml
<use_store translate="label">
<label>Add Store Code to Urls</label>
<frontend_type>select</frontend_type>
<source_model>adminhtml/system_config_source_yesno</source_model>
<backend_model>adminhtml/system_config_backend_store</backend_model>
<sort_order>10</sort_order>
<show_in_default>1</show_in_default>
<show_in_website>0</show_in_website>
<show_in_store>0</show_in_store>
</use_store>
Note, you should not change this file directly, but overrie it in your own module. You can find many tutorials out there for helping to override core magento configs and files.
if you updated the scope settings:
<show_in_default>1</show_in_default>
<show_in_website>1</show_in_website>
<show_in_store>1</show_in_store>
this will allow you to change the "Add Store Code to Urls" for each website/store front in the admin section.
Now you can try and set "Add Store Code to Urls" = NO for the default store
and "Add Store Code to Urls" = YES for the others.
Please note I have not tested this, so I would not do this on a live store :)