Hi Miri,
In my experience, deleting .glock files did not have unintended consequences on the system/ArcGIS Server, though this was always done as a last resort and in a surgical fashion (i.e. only the .glock file for a single locked-up service was deleted). Once these files are removed, it is possible to administer the related services and return them to a usable state.
You may run into a situation where the ArcGIS Server Java process (javaw.exe) has hooks into the .glock file that will prevent you from deleting it. In that case, you will either have to restart ArcGIS Server (to release its hooks in the file), or use "kludgy" tools to force that same release. Of course, if you are running in a production environment then restarting ArcGIS Server is less of an option and you may have to turn to tools like this one.
On a related note, there is a bug number for this problem (NIM100965: "Starting a service with 0 minimum instances causes the service locks not to release if service is consumed while it is starting"), and the Issues Addressed List reports it as being fixed in 10.3.
I was able to reproduce this issue on a pristine server and install of ArcGIS Server (10.2.1) by creating a high-isolation Map Service with 0 minimum instances and then rapid-fire reloading the service's WSDL URL while the service started.
Hope this info is helpful to you.