Hello,
Reboot of the machine will be required always when upgrading from SEP 11 to 12.1 - this is normal and expected due to differnced in the architecture of both versions.
However, you can check the article below to create packages in SEPM 12.1 for SEP clients.
Where to (How to) configure the client Restart Settings in SEP 12.1 - options available
http://www.symantec.com/docs/TECH177107
Create the SEP Package with the same settings of NO RESTART.
Check this Article for the same:
Creating custom client installation packages in the Symantec Endpoint Protection Manager console version 12.1
http://www.symantec.com/docs/TECH165801
If you are planning to upgrade or migrate to Symantec Endpoint Protection 12.1.3, please take a look at the latest how-to article created by our very own SEP content council team.
Best practices for upgrading to Symantec Endpoint Protection 12.1.x
http://www.symantec.com/business/support/index?page=content&id=TECH163700
Hope that helps!!