Just introduce the Contessa as the lead Shield agent in the series, she doesn't have to be the Deputy Director, but she could be a senior agent with her backstory with Fury kept intact.
I'm sure Joss knows what he is doing. His wealth of knowledge concerning the Marvel Universe is well known by now, so I have no concerns about the series or investing in any new characters that will be introduced to us in the series.
If this series does well, I can see them making Maria Hill a regular. Cobie Smulders' current show, How I Met Your Mother
is expected to end next season.