I agree that not all people will have problems with wire transfers. I still believe Black Arrow would be better to make BTC price totally transparent by taking the payment straight away. These decisions are already difficult to make, why make it even harder?
I know one of the big issues I know they have been having is being understaffed- To many tickets with too few people. As for using BTC-e, not sure why that was chosen, could be for money could be because thats the easiest exchange to get $ into via wire? Not sure, I only use CB or Local for all my BTC.
I think it may actually be the worst place to get USD into, take a look at the Scam Accusations thread. This is said to be the reason that the BTC exchange rate is so low on btc-e, because there is low confidence that the USD wire will arrive in your btc-e account.
Out of interest, what stage of the process do you take customer BTC on your site? As part of placing the order, or an indeterminate amount of days after placing the order? I suspect the former, as this is the norm with all BTC webmerchants.