I'd think that a hunter-killer warship would have a good capacity to work independent of a supporting fleet for a long time (i.e. a few months). It would have a really advanced sensor suite, perhaps with some good stealth/EW tech.
Rather than having a lot of guns all over, it'd have just a few powerful beam cannons on a close spot on the ship; probably a broadside so it wouldn't collide with debris when it jumped out. It wouldn't go for prolonged fights; it would have to be a jump in, unleash beam salvo or two, jump out. The armor wouldn't be to strong, but the engines would be really powerful; powerful enough to get a corvette sized ship to 40ms and jump drives recharged in 1-2min.
This way, you jump straight in next to a destroyer and her escort, you unleash two salvos of three Bgreens and jump out before too much return fire. The enemy wouldn't see you coming too much because of the stealth tech, and hopefully would be caught by surprise.
I figure past that, it would have a small bay for a squadron of fighters for recon, and possibly escort if situations become dire, but it would probably be ships like the Loki.