Smallville Continuity

[Possible SPOILERS]

As I've repeatedly noted, I just got into Smallville a year or so back, so I'm no expert on the series. That being said, I have seen pretty much all the episodes in reruns and I've been noticing what seem to be some glaring inconsistencies from earlier episodes.

Today's rerun (ABC Family) was entitled Truth and in it, Chloe is exposed to a chemical which causes her to exude pheromones which force the people she speaks with to tell her the truth - even if they don't mean to. She asks Lionel (Luthor, Lex' dad) at one point if he had his parents killed and he said he did, for their insurance money which he needed to start his business.

In this year's season finale, we learned that Lionel is actually an ally of Jor-el's who is looking out for Clark. Well, he was searching for the Kryptonian sent to Earth and was pretty certain Clark was him, but was still trying to make sure. Then he helped Clark and J'onn Jonnz (Martian Manhunter) fight Lex and Bizarro.

Now, that's all well and good and certainly a great twist. I have no idea how close to the comics this all really is, as I was never a big Supes fan - so sorry, but Captain Boy Scout just never did it for me once I got old enough to realize he had pretty much every power in superhero comic books - but it certainly makes for good TV. Still, there have been a lot of things throughout the series that hint at the fact that Lionel Luthor is a bad, bad man.

Now, is he just going the distance to do his alien job - a general lack of concern or remorse for human beings is what is implied - or is this new development of Lionel as "anti-"hero going to turn out to be a red herring? As for the latter, I'd find that hard to believe, since Martian Manhunter confirmed his job; in fact, without Jonnz' confirmation, Clark would never have believed Lionel...

I know, "It's TV," but in a show so good, you know as well as I do that they probably don't just have one person doing Continuity - especially if they are holding somewhat close to the established story followed in the comics. I also understand that even comics tend to rewrite their histories from time to time, so that's not really the question. The point is, I'm not sure what the hell is going on over there in Smallville. Anyone?