I actually gave my prediction a few days ago in another thread, the smallville (spoilers) thread in Off Topic. Surprisingly I was right. I'm not usually right about these things.
They actually killed Jonathan in an appropriate way. Canon actually did have Jonathan dying of a heart attack. They tried to fool us into thinking the traffic accident was the cause of death of the one who would stay dead.
Two good things came out of that episode. One, we at least got to see Lana die, even though she didn't stay dead. And two, it seems Clark's highly unlikely to ever risk telling Lana his secret, which means they're finished as a couple.
It's kinda nice that most of us hate Lana. Keep in mind that we couldn't believe that it took two years for Lois and Clark to get together in our favorite show. Yet five seasons of "torture in Smallville" have Lana and Clark still going through the "will they or won't they" syndrome. If we actually liked Lana, we'd have been driven insane three years ago.