You don't have to restart the entire cluster. While launching the cluster, you can specify a hive-site.xml file with the details of RDS. If you are not following this option and making the changes manually after launching the cluster, you don't need to restart the entire cluster. Just restart the hive-metastore service alone. Hive metastore is running in the master node only
You can launch the cluster either by using multiple ways.
1) AWS console
2) Using API (Java, Python etc)
3) Using AWS cli
You can keep the hive-site.xml in S3 and perform this activity as a bootstrap step while launching the cluster. AWS api is providing the feature to specify custom hive-site.xml from S3 rather than the one created by default.
If you are using hive from the master machine alone, you don't have to make the changes in all the machines.
An example of specifying the hive-site.xml while launching EMR using aws cli is given below
aws emr create-cluster --name "Test cluster" --ami-version 3.3 --applications Name=Hue Name=Hive Name=Pig \
--use-default-roles --ec2-attributes KeyName=myKey \
--instance-type m3.xlarge --instance-count 3 \
--bootstrap-actions Name="Install Hive Site Configuration",Path="s3://elasticmapreduce/libs/hive/hive-script",\
Args=["--base-path","s3://elasticmapreduce/libs/hive","--install-hive-site","--hive-site=s3://mybucket/hive-site.xml","--hive-versions","latest"]