I really feel for you if you have got something unexpected, though it is important to understand how the vouchers work when you purchase them to make sure you get what you are expecting.
When you purchased your "two" vouchers, did you do this:
a)
View attachment 25665 x 1 (once)
or this:
b)
View attachment 25666 x 2 (twice)
If (a), then what you purchased was one voucher which is for two people, and the value of the voucher is $500 per person (thus $1000 total voucher value). In this instance, yes, both people have to book/travel together.
If you did (b), then you should've received two vouchers for one person, and each voucher is worth $500.
Did you receive one or two voucher reference numbers? If one, then you did (a); if two, then you did (b). If (a), then what Qantas is saying is entirely correct, and (while I'm not a lawyer and not involved in consumer protections etc.) there may not be much you can do.
If you really can't use your one voucher for two people, you may be able to offer it on eBay to someone who does want to travel with two people where their flights are a minimum of $500 per person: you can change the name of the travellers at the time of booking after all: you would be "gifting" the gift voucher to those travellers (of course, I guess you would want those people to pay you your money back).
Hope this helps.