After trying to bait them into wrapping up the current adventure arc (and speaking to them about it metagame via email), they didn't go along with it. Last night's session, for which I prepared about 8 hours, ended up being a series of confusing discussions about why they shouldn't attack the BBEG. ("We don't have enough proof," "things are too ambiguous," and "what if he is too tough.") What was intended as a straightforward combat that should have taken 30-45 minutes and lead into the "rest" of the adventure (a typical save the small town vs. the evil humanoids mission) was instead replaced with split party investigations, going to brothels, visiting orphanages, street preaching, breaking into buildings - all done by individual characters with no clear goals in mind.
I try to make things as straightforward as possible, but they always find ways around it. The villain in this case was a LE manipulative type, and they totally bought every thing he said (even though the group KNEW he was evil and was trying to destroy the city).
I don't know. If the villain is a master manipulator who is successfully convincing them of things that are not true, then it may well be you aren't making things as straightforward as possible.
You really can't have it both ways - if you use a villain based around deception, and he succeeds at deceiving the PCs, you can't then go ahead and blame it on them. I'd take a step back, and either drop convincing proof in their laps that truly gets them to take action, or switch to using genuinely straightforward villains.
Outside of that, as others have said - did they enjoy the session? That is the important part, more than whether they went down the proper adventure path that you had planned. Taking the current adventure away from them and tossing them on another, because it didn't go as planned... I'd consider that carefully before doing so, if they are truly enjoying the game as it is now.
Which isn't to say that you need to keep running a game you don't enjoy, of course. But I'd certainly talk it over with them first.