A very interesting question indeed!
I am no Buddhist, but I too thought it a little cruel to go around killing the queen every couple of years, just because she might fail to service my exacting requirements for honey production.
I think that is what it comes down to - for what reason do you want to keep bees?
If it is for honey production, as I think it probably is for most people, then killing the queen is pretty much required - in just the same way as it is "necessary" to kill battery hens when their productivity drops.
If, on the other hand, you are in it for the joy of beekeeping, from an ecological point of view etc. etc. (as I suspect you might be), and honey production isn't the most important thing, then why not simply leave your hive to it?
Leaving the hive to look after itself, with no killing of the queen will result in lower honey crops, as your hive will swarm more often, but if you are happy with that - it is the more "queen-friendly" approach!
I'd be very interested to hear what you decide - this idea has rather sparked my interest!!!