Shibboleth IdP is a java web application (as explained on their wiki for instance). So yes, you need to run a server (servlet container) for it to function at all.
Not using Jetty is possible, but then you would need an alternative, such as Tomcat, so that doesn't solve your 'problem'.
If you need to start it manually using ssh, the system has probably been rebooted? What you would typically do is to make sure that when a system starts, it also starts all the background processes that you always need (jetty with shibboleth installed in your case). See for instance Auto run Jetty on boot.