Yes, make a CD image file of your Freelancer transfer it to your server using such protocol as FTP or HTTP or SCP or whatever suits your situation, mount the image files using a program such as
Daemon Tools and install your software. However, you need a method of remote access GUI, such as VNC, Terminal Server or Remote Desktop to install your freelancer server, afterwards you may turn flserver.exe into a system service and no longer need means to remote access the server's GUI. And something more I hope you are refering to a server using a Microsoft operating system, otherwise.... the answear is a big
NO
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3NET Freelancer Server Admin
See server forum
here.
See server stats
here.