The work E-mail address you entered is already associated with a different Apple ID. Please, try a different Work E-mail
You have two options if your company has no prior VPP set up. 


Choose a different email string to register.
Log in to the email you wish to use at http://appleid.apple.com and change the ID/email to get off the one you wish to use for VPP.


The VPP portal does things to the AppleID you enroll that isn't handled/allowed for pre-existing accounts. Unless you can substitute a new email for the one you want, you're really bound to choose a new account.

Now, if you are trying to register a second VPP you will run into many different problems. First exhaust internal measures to recover that account or work with the holder of that AppleID. 

In your case, the responsible person has left the company, have you contacted them to see if they turned it over to someone or left the password written down with their other papers?

If not, you have options:


Contact IT and explain you need to get access to the former employees email account. Offer to handle the password reset or provide them the Apple links and assist them if it's faster. I've brought a pie or brownies to ensure the IT staff are properly motivated to help me out. :-)
Have HR contact the employee and ask if they turned over the password to this account and arrange to have that information returned to the company. If that fails, contact legal and request return of the company property (the company VPP account).
If that fails, have these people write up their efforts and take that to your Apple Representative. If you don't have one, contact the local Apple Retail store and ask to speak with a business representative.


I've never seen a case where someone couldn't get control of an Apple ID, but you might need to do some work to prove you are now the rightful company contact to get traction. Working with people you can see in person or face time with is far easier than 1-800-APL-CARE in my experience, but even over the phone with the right data and patience, you can often get what you need or have your problem escalated appropriately to a person that can help you.