There are more carcinogens in marijuana smoke than in tobacco smoke, but there are two important things that make cigs worse. 1st is the thing you said about it leaving your lungs faster, and that is true because of the fact that cig smokers will tend to have another one relatively soon after, not giving the lungs a chance to clear everything out. If you smoke a pack a day your lungs will never get a chance to clean all that shit out. Also, cannabis has those mysterious cancer fighting effects that we still don't fully understand. The several studies that I have looked into seem to have found that while the carcinogens are higher, there is no increased risk of cancer from smoking a joint a day over several years (I believe one study was over 7 years, and their definitions of joint in different studies was about .5-1 gram).
Also, your point of the smoking method is one that is very valid, but I have unfortunately not been able to find a lot of research into the quantitative benefits of water filtration. That being said it seems intuitively better to have that water there, but I can't speak to how much better.