We have about 6000 machines with Panda Endpoint Protection (v7.2) and we are planning to switch for SEP. Will SEP installer uninstall Panda automatically or does someone know a good solution for this (script or something already tested method)?
The installer itself will not but you need to use SEPPrep which will run before the installer.
The full details are here:
Uninstall third-party security software using SEPprep
http://www.symantec.com/docs/TECH148513
there is new feature intorduced in SEP 12.1 RU1 MP1 which will let you to uninstall third party anti virus, before installing SEP. this article is updated only until SEP 12.1 RU5 and after that there were four other version released the most recent version being SEPM 12.1 RU6 MP2. SO I would suggest you to try deploying the recent client from SEP 12.1.6 MP2.