Got to say the back and forth on this has been...odd. Im glad you are not writing up a new army and rules. I dont mind people doing it but way to often there is little balance.
I to am making a Sisters of Silence army. I will start a
PM about it soon (once I get some parts). Im caught right now between using the Sisters of Battle or Grey Knights as the "count-as" rules. Both have appeal, but it could come down to cost / conversion work. After the first (5) models are created then I will decide on the rules
lol. Anyways, the
SoB seem like the best option due to the Shield of Faith rule. The agents you see in the books I gather are the most "gifted" and are fielded in small numbers.
Fielding an army size force, you will likely encounter less "gifted" agents, if you will. I would look up the card art for the sisters here:
http://www.pa-sy.com/hhccg/
That will give you the name of the squad types and allow you to correlate with the current armies. Good luck.