atlantis didnt fire back because they were almost out of drones + lacked power for the chair...
and about the size of ships, here is a quote about wraith hives:
portal: stargate, on wikipedia wrote:Wraith Hive-Ships are the second largest known ships in the Stargate universe, after the Ancient city ship. It is even larger than the Ori battlecruiser as seen in the SG-1 episode "Camelot". Hive ships are at least 13 times larger than Earth's Daedalus class battlecruiser. It is unknown precisely how many Wraith each hive ship can carry, but the number is well into the thousands.
and about the weapons, the ori used several minutes to beat the shields on the "Korolev", yet read below, in bold text:
portal: stargate, on wikipedia wrote:A Wraith Hive-Ship has a large number of weapon ports stationed across the exterior of the ship. These ports rapidly fire blue energy bolts which are powerful enough to destroy another Hive-Ship after around 20-30 hits and, when several Hive-Ships worked in concert, were able to bring down the Asgard designed shields of the Daedalus in less than a minute. The ship does not seem to have any point defense weapons to fight off smaller ships such as F-302s. Instead the Wraith Dart is used for fighter-defense. It is not known how many fighters can be carried by a Hive-Ship, but it is estimated in the hundreds as shown in "The Siege" and other episodes.
the wraith do have telepathic powers, remember how they control their ships, and also how they can control each other and some humans... they can also be very "persuasive", forcing people to kneel... at least queens can do that...
no doubt the ori would construct some virus, but the wraith have almost perfect health, so the only kind of virus that would affect them would be asuran-style nanites, and they have a will of their own, and only strike when they want to...
while the lack of mental powers may make it harder for the "good guys" to defeat the ori, it is not impossible... remember, they did destroy 1/4th of the ori army... so it is not impossible...