Before you'll point me to http://social.technet.microsoft.com/Forums/lync/en-US/10ac1e4c-f991-43b6-b8e6-6996b1e2740c/disable-calltotel-link-registration?forum=ocsclients or http://social.technet.microsoft.com/Forums/lync/en-US/5de1b4bb-1d07-48f1-a6f9-fdae5befac6d/lync-stealing-callto-and-tel-protocols?forum=ocsclients - those are for Lync 2010 where it used to work, but Lync 2013 doesn't even have that registry key anymore (there's no Communicator key under Microsoft... and creating one does nothing).

We use Lync 2013 as collaboration utility, but telephony is done using another system, and without enterprise telephony, it makes no sense that Lync 2013 retakes those url associations.

So, how can this be turned off for Lync 2013?

Go to Control Panel\Programs\Default Programs\Set Associations

And change the default program for TEL to whatever you want it to be

Hmm... that works, let's say, partially. The OS now launches the app I want (had to extend the app so it would provide all the necessary info to show up in programs and defaults first), and it works in IE and Firefox, but Chrome still defaults to Lync (it seems it looks in HKCU\Classes, and using the programs and defaults modifies HKLM\Classes)

Try to modify the default value of (default) under the path HKEY_LOCAL_MACHINE\SOFTWARE\Classes\tel\DefaultIcon