I think Malfoy might have had an idea about what Voldemort had done to protect himself from death, (i.e. the horcruxes) but I think you're right. He didn't want Voldemort to come back, per se, because then he would be beholden to him again. And Lucius Malfoy doesn't strike me as the kind of man who wants to live his life doing the bidding of another (extremely insane) person. I think Malfoy just wanted to get rid of some stuff that might connect him to Voldemort, because the ministry was getting ready to raid the houses of known Death Eaters again. And Malfoy was a known death eater.

Of course, he could have known about what the diary could do, because why else would he put the diary into a student's cauldron? Maybe Voldemort had left instructions for Malfoy before he died, that in the event that something like this happened (i.e. his "dying"), he was to take the diary to Hogwarts as soon as he was capable, thus sparking the catalyst that made the Chamber of Secrets open.