AWS Elastic Beanstalk is designed for deploying your running apps in a way that is designed for scalability from the ground-up. Because of this, Elastic Beanstalk will launch one or more EC2 instances, connect them to an Elastic Load Balancer instance, configure CloudWatch monitoring and Auto Scaling triggers.
Also, because of its fundamental design for scalability, Elastic Beanstalk is designed around a one-app-per-environment model (whereby "environment", I mean one of these EC2 + ELB + CloudWatch + AutoScaling clusters).
Since running two separate web servers with two separate apps (PHP & Java) is not a fundamentally scalable design, it's not a use-case that Elastic Beanstalk is optimized for.
You are free to spin-up a standalone EC2 instance and install whatever you'd like on it, but you're right — git aws.push
support has not been made available for standalone EC2 instances. If the git support is important to you, you'll need to weigh the pros and cons of each approach.