Well, despite things, I think it's stated Lavos had some measure of sentience. While stuff like destroying Zeal, attacking Magus, and the 'Destruction Rains from the Heavens' of 1999 can be attributed to instinct reactions, there is the fact it took Chronopolis back in time as a precaution from the time travelers that wanted it's destruction. While acting on the instinct to survive, there is the fact the measure it took is much more complex than all the ones used before and does needs some level of intelligence for it.
But then again, since it evolved throughout the years, it could've very well gained it at some point, especially since human DNA was part of the harvest.
Well, in any case, I'd say the biggest mistake was sending the Gurus through time. Considering how many things couldn't have been possible if the Gurus hadn't been where they were sent to.