You can only do it on DB at the moment.

1. SQL

Either ...

UPDATE core_config_data SET value = '1' WHERE path = 'dev/template/allow_symlink';

Or if entry does not exist ...

INSERT INTO core_config_data (config_id, scope, scope_id, path, value)
VALUES (NULL , 'default', '0', 'dev/template/allow_symlink', '1');

Note: Don't forget to add table prefix if you use one.

2. Script

Or run this from magento root ...

<?php
require_once('./app/Mage.php');
Mage::app();

Mage::getConfig()->saveConfig('dev/template/allow_symlink', '1', 'default', 0);

3. local.xml

Add another XML to app/etc/ directory like local.SUPEE-9767.xml to override local.xml.

<?xml version="1.0"?>
<config>
    <default>
        <dev>
            <template>
                <allow_symlink>1</allow_symlink>
            </template>
        </dev>
    </default>
</config>

4. "Module"

Create a mini "extension" with this system.xml to bring back config option to admin backend:

<?xml version="1.0"?>
<config>
    <sections>
        <dev>
            <groups>
                <template>
                    <show_in_default>1</show_in_default>
                    <fields>
                        <allow_symlink>
                            <show_in_default>1</show_in_default>
                            <backend_model>core/config_data</backend_model>
                        </allow_symlink>
                    </fields>
                </template>
            </groups>
        </dev>
    </sections>
</config>

Add an empty class for backend_model to enable save config value. Thanks to @colinmollenhour, instead of an empty class just reset backend model to parent.

^{Download: https://github.com/sreichel/magento-StackExchange_AllowSymlink}