1. Slavery is worse than murder. I'd rather accidentally kill than be a slave owner. The fact that these two acts are being compared shows how necessary it is to examine the practice of beekeeping. It is the blatant exploitation and the fact that bees are treated as machines that make the whole enterprise so bad, not merely the fact that bees are killed.
2. Nobody's perfect. I don't know any vegans who claim to be perfect nor do I see what the big deal is. The main idea behind veganism is a movement toward veganism and away from animal slavery. The fact that we can't avoid all harm to animals is certainly no argument for deliberately exploiting bees.
3. No intent to kill. It is impossible to travel and not kill bugs. Whether one steps on them, rides over them on a bike, or they get smushed on the windshield of a car or bus, bugs die when people move. I don't think any level-headed person would honestly expect vegans never to venture out of their house in order not to kill bugs. In contrast, beekeepers routinely kill off their hives in the fall because it is cheaper than housing, feeding and keeping the bees disease-free over the winter. There is zero value attached to the bees; it is only their ability to produce honey that is important. Other beekeepers don't intentionally kill bees, but it is obvious many will die at the hands of the beekeeper that wouldn't if the human never got involved.
4. Yes, at some point, humans are more important. The worst case scenario, say a vegan calling an exterminator to kill termites that are destroying her home, has virtually nothing in common with beekeeping. The vegan did not purposely breed the termites nor did she exploit them while alive. It is extremely unfortunate that the situation was not prevented (and vegans should be more aware of how to do this) but she is under no moral obligation to simply stand by and watch her house be eaten. (Or, say, to watch her scalp be eaten by head lice.) In some cases, killing cockroaches (or vice versa) may under the category of a necessary evil.
5. Stop the slaughter then! Vegans should make more of an effort to prevent unwanted invasions and know how do deal with other animals in a non-violent way. Check out Getting Rid of Pests from The Vegetarian Society UK.
6. Shame on you. The real reason why people (in whatever context, not just a discussion about honey) bring up the subject of killing bugs is because they are trying to deflect their own shame about killing animals by attempting to shame vegans. The appropriate response for a vegan is not to ridicule the meat-eater by going on and on about how many more animals he kills, but rather to acknowledge your own shame about not being able to be perfect.