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I'm not aware of the Sisters having any ships of their own, so probably do like the Inquisition, using the same ship classes as the Imperial Navy. The sisters are fairly well equipped but their resources pale in comparison with the Space Marines and (especially) the Inquisition. As such a 'typical' Sororitas force would be made almost exclusively of small to midsize ships like Light and Medium Cruisers at most. Larger vessels would be extremely rare, say 1-2 at most (total), as they would be among the most Sacred Relics of the order. Not to mention the most ornate/decorated models in the fleet. Sororitas banners and Purity Seals, etc., fom 40K should adorn each "Big Ship" from Heavy Cruiser on up, that you choose to make for your Fleet.
Ruleswise, what Grey Templar suggested is best. Mind you, not all players are willing to accomodate alternate rules, so have 2 Fleet lists for your force; 1 Standard Imperial Navy rules, 1 modified with the +1s mentioned above. Also i've seen in threads here about Full Thrust and other game systems used as a stand-in or anternative to BFG, using BFG/GW fleets. So you may want to give one of those a try sometime.
I hope that helps! Good Luck and Happy Modeling!!
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