Chuck saw Lilith with Sammy but if Sammy hadn't burned the hex bags Lilith wouldn't have been able to find them...Sammy, however, wanted to face off with Lilith..I don't feel like their free will has been taken away...I feel like Chuck simply sees what the boys will do..
if they hadn't known what was coming they would have made the choices that were outlined in the books..those choices were their free will and it was only in knowing what was coming that made them question those choices..
anyway, the episode also shows that they have free will on parts of the story that haven't been written about and it's possible that free will is what blocked Chuck from seeing what happened after Lilith shows up in the motel..he didn't write the stuff about Dean taking him to the motel and confronting Lilith..

I completely agree with you Lucy!I think that the boys have free will but Chuck - the prophet has foreseen their choices.However,in the last episode we saw that even though they made different choices from what they would do in normal cases without knowing what's going to happen,what was written happened (eg the bacon burger,Red hotel etc).Besides,we saw Zachariah mentioning at the end of the episode their ''destiny'' that will definitely take place and that they shouldn't know ahead of time about it.So, I'm wondering if Sammy wants to stay on the good side isn't there any hope that he won't go to the dark side?

Of course there's always free will.This show is all about choices.As lucy and toti8 said,Chuck just sees what happens.The difference is that their actions lead them to their destiny,which is to face Lucifer.

I agree, lucy- Chuck isn't dictating what's going to happen, he's just seeing it. Also, both Sam and Dean went off script. Chuck said that Sam was supposed to have sex with Lilith- but instead he went for the knife to kill her. Chuck didn't see Dean showing up to drag him to confront Lilith. Those things weren't in the script, the boys changed it. So I think they can still change their fate!

You guys said it all! I believe they can and will alter their destinies; the greatest gift to mankind is free will.

I'd like to think that show is going to allow for free will. If you look at it everywhere they went was because they knew what was going to happen. Would those things have occured if they hadn't been trying to run from the prophecy about lilith.

Well, we did see just a touch of it in TMATEOTB.