"The company claimed that it was permitted to claim back the VAT it had paid on the purchase of the vouchers, but not account for VAT when giving the vouchers to employees."
What do they mean by "account for VAT" as given above?
If it means charge the employee VAT then it is arguably a bad judgement*, but if it means something like take the VAT amount into consideration when calculating the value of the vouchers with regards to salary sacrifice then I don't see a problem with that.
*Remember though children, even at 17.5% or even 20% VAT you will still be making more money out of the exchequer (for that read "the rest of us who pay tax") than you would if you had paid income tax and NI on the voucher but no VAT. Especially if you are a higher rate tax payer.