I don't think there is any reason why they can't be in continuity. Well, besides the fact that World of Smallville said that Jonathan was in WWII, when it's been said recently that he was in Korea. I like it better that way, because it makes the Kents around 60 instead of 70(and that my great uncle was a POW in Korea like Jonathan!). And I assume that you're referring to the bombing of a Kryptonian city by the group Black Zero as the inadvertent cause of Krypton's destruction. I don't see why that can't be in continuity either.
Benjamin Grose, a.k.a. Kryptonkid
http://www.bigfoot.com/~kryptonkid Larry: 'Bob, I don't have any handths!'