How can I create an attribute as "not configurable" from an install script?

If you go through the Mage_Eav_Model_Entity_Setup::addAttribute() method, you can find that the options are getting filtered in the Mage_Eav_Model_Entity_Setup::_prepareValues() method.

The _prepareValues method only allows the following options to go through:

'backend_model', 'backend_type', 'backend_table', 'frontend_model',
'frontend_input', 'frontend_label', 'frontend_class',
'source_model', 'is_required', 'is_user_defined', 'default_value',
'is_unique', 'note', 'is_global'

Any option that needs to be set, and is not in previous list, cannot be passed into the addAttribute method.

The only exception to those are: sort_order, group, user_defined and option. Those are used independently from the _prepareValues method.

One way to work around this issue, is to update the attribute after it is created, using the Mage_Eav_Model_Entity_Setup::updateAttribute() method.

$this->updateAttribute(
    Mage_Catalog_Model_Product::ENTITY,
    'size',
    'is_configurable',
    false
)

You should actually use Mage_Catalog_Model_Resource_Setup::addAttribute()
instead of Mage_Eav_Model_Entity_Setup::addAttribute()

As you have found out in the code, Mage_Eav_Model_Entity_Setup::addAttribute() only allows the following options:

backend
type
table
frontend
input
label
frontend_class
source
required
user_defined
default
unique
note
global

Whereas Mage_Catalog_Model_Resource_Setup::addAttribute() allows all of the above, plus the following options:

input_renderer
global
visible
searchable
filterable
comparable
visible_on_front
wysiwyg_enabled
is_html_allowed_on_front
visible_in_advanced_search
filterable_in_search
used_in_product_listing
used_for_sort_by
apply_to
position
is_configurable
used_for_promo_rules

You can use this class even if you have defined another setup class in your config.xml:

$installer = $this;
$installer->startSetup();

// Create your tables, etc

$catalogInstaller = Mage::getResourceModel('catalog/setup', 'catalog_setup');
$catalogInstaller->addAttribute(Mage_Catalog_Model_Product::ENTITY, 'size', array(
    'type'                       => 'int',
    'label'                      => 'Color',
    'input'                      => 'select',
    'required'                   => false,
    'user_defined'               => true,
    'searchable'                 => true,
    'filterable'                 => true,
    'comparable'                 => true,
    'visible_in_advanced_search' => true,
    'is_configurable'            => false,
));

$installer->endSetup();