My company has a vpn setup like www.companydomain.com/vpn. I believe they are using Juniper based VPN. Now would I be able to connect my Motorola Photon to my company VPN?
You shouldn't have a problem. I've never used the VPN option on the Photon but as long as you configure it properly it should work.
Settings > Wireless & networks > VPN Settings
Take your phone to IT. they could have never set it up for a phone before, just ask them for the exact, in stone, configuration settings that anything connecting to your VPN will need to use.