I am pretty sure the security bond is for the total of £109,000 so you get the whole £109,000 paid back to you over the 9 years.
Looking at the EasyJet MPL their security bond is £69,000 with further training costs on top of it - which is why you only get the £69,000 back through the bond.
In regards to the question about whether it is tax free, it is taxed differently to your normal salary - it is tax efficient to both Virgin Atlantic and the Cadet. I cannot say exactly what the tax rate is, but it is desirable!
Any interest on the loan (I have calculated it to be around £23,000 - but this is an 'guesstimate') you wouldn't get any help from the security bond payments.