If you are saying that you changed the igateway.conf file to restrict EEM iGateway to TLSv1.2 with the <secureProtocol> tag, then for Process Automation you will have to add a line to the c2osvcw.conf file at in addition to upgrading Java.
If you are currently using a 1.7 release of Java, you must upgrade to update 95.
If you are using a 1.8 release, do not use release update 91 or later.
At the end of the c2oscvw.conf file, add this line:
wrapper.java.additional.14=-Djdk.tls.client.protocols=TLSv1.2
Ensure the number used is sequential to the last entry in the file.
If you are going to be restricting your network at the OS levels to only TLSv1.2, please get in contact with CA Support. There are a number of other things that must be considered, and EEM will have to be upgraded to the new release due out soon which is 12.51 CR06. I do not have an ETA for that, but it is coming very soon.
~Jenn