You may need to lower the rent to minimize vacancy loss and get a larger pool of potential renters but you will rent the apartment (with minimum vacancy loss).

To my simplified way of thinking the only disadvantage is the cost, which in all honestly is pretty minimal.

Could be a deal worth doing, but it might take a couple years to increase rents to market rates and minimal vacancies.  

I've always been able to get a preapproval based on minimal info about the offer price and the property address.

Minimal 21 day inspection period.

For a single home the fee will be very minimal. 

However, the advantage of the commercial loans is that closing costs are a lot less so the am length is really minimal. 

What would be our best option to minimize out of pocket expenses on the deal?

Are the returns on the duplex minimal and could you get a better ROI elsewhere?

You can contact the local housing authority to see if the voucher can be used as any leverage, but you need to keep in mind that a.) you will likely never collect the money if she moves out, b.) your prime goal is to get the tenant back on track or to get possession of the property back and minimize your losses.