Developing NMS using PHP

Actually my team is developing a Network Mangement System with GUI in PHP. The Server is LAMP basically. Most of the interaction between NMS server(in JAVA & SNMP) and GUI(PHP) is through flat files and DB only. Since the project is very dynamic and very interactive, we are using ajax to populate the data that the NMS server has gathered. Also most of the processing of the gathered data is done using shell scripts(since it is very fast and easy for us to do in this way) to get interesting analysis results. Some of the requirement is like that on click the shell script should be invoked and do most of the analysis work or on the recent data gathered. The GUI also has to incorporate the user mangement and Configuration management of the server and other network devices.
I am a new PHP developer don’t have much experience. I want to ask that is it the right and secure way of doing things what we are trying to do. We are fluent in shell scripting so for every configuration and management work we are invoking the specific scripts on the click to handle the work. I think that our project is more like enterprise application solution that should be developed in J2EE instead. Does the PHP has capability to build this type of solution also.