I think that you may be looking at this in the wrong manner.

As a agent for Sanlam, you made the sale on the behalf of Sanlam. The customer is paying Sanlam directly, because Sanlam is sending the invoice directly to the customer, and in that payment, it has the VAT portion.
YOU DID NOT MAKE THE SALE. You were instrumental in making the sale, there for the commission provided by Sanlam yo you, will not include VAT, as there is no sale that you made to Sanlam. They are providing you with a payment as commission for the original sale made. This is the reason that Sanlam will not provide you with a VAT invoice, but a statement that you received income. When you enter this income in your books, it will be a zero rated VAT output.

This is a similar manner in which Prepaid Electricity is handled by shops who are agents selling prepaid electricity.
You will need to make an entry on your VAT form, as the income received from Sanlam as zero rated sale, and is a separate figure from your output VAT figure..

I hope I explained it properly here.
Maybe you should approach a SARs office, and allow them to explain it to you.