There's no question that sometimes it's necessary to consider pest control even for bees. If the bees are Africanized, the so called killer bees and are very aggressive it is probably a good idea to consider this.
I once had a lady call me to remove some bees from a tree outside her front door. It transpired that her husband had been told by his doctor that his next bee sting might be his last. I felt that the only sensible thing to do was to call a local exterminator. It wasn't worth risking the man's life to save a colony of feral bees.
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In some cases it's possible to encourage a newly arrived swarm of bees to move somewhere else. I've blown smoke into a cavity with my bee smoker, as long as the bees haven't established themselves in their new hive, the honey bee smoker sometimes does the trick, but be very careful of the sparks which smokers often produce.
If it's found necessary to actually kill the bee colony I would not advise a do it yourself pest control solution, however I would urge you to look for home pest control reviews, it might be possible to find an organic method. My wife swears by a sonic pest control device to keep mice away and her version of spider pest control (we have black widow spiders and brown recluse spiders) is to squash them. I'm not sure this would be effective for bees but I would hope a non-toxic extermination option would be available.
I'm sure no-one wants to kill an apparently healthy colony of honeybees, we need bees so desperately to pollinate the food we eat, however if a colony decides to invade a house I think an exception has to be made. I don't kill bees, I don't advocate this, but sometimes there's really no alternative. I've spoken to San Diego pest control companies and one of their main concerns is the Africanized bees they encounter.