Ok, I think I've found a solution. It could not be related, so feel free to 
remove my comments in case they're misleading.
I had to add a config file in /etc/polkit-1/localauthority.conf.d/ named, for 
example, 52-ldapsudo.conf. It contains the needed line to instruct polkit to 
use the right groups. Like this:

[Configuration]
AdminIdentities=unix-group:unixadm


Where unixadm is a group with admin permissions.

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https://bugs.launchpad.net/bugs/892680

Title:
  PAM with LDAP breaks authentication to Policykit enabled  Gnome
  applications using LDAP credentials

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