Multisite - Put one alias in maintenance mode We have one installation (let's call it example.com) with two domains (development.xpto.com and example.com) serving as alias (defined in sites.php) to the main site folder.

We wanted to put one of those aliases (the example.com) in maintenance mode and leave the development domain working np.

What's the best course of action to attain this functionality?
If your multi sites have separate databases than you can simply put whichever (sub)domain you desire into maintenance mode without effecting the other domains. 

If you are using the Domain Access Module, you should navigate to that domain's maintenance page and put it in the mode you desire at subdomain.example.com/admin/settings/site-maintenance - see my screen capture