To create an intentional false dichotomy: if I have to choose between a site that surfaces all content regardless of controversy but accepts that related discussions will be lower-quality, and a site that directly or indirectly suppresses some content to maintain higher-quality discussion overall, I will choose the latter.
I appreciate that some people feel that the "loss" of some submissions due to automatic flamewar detection algorithms or user flagging is a problem, but I, for one, appreciate that the discussions that remain on the front page (for a long time) have a reasonable guarantee of being high quality.
Relatedly, it may also have an effect on the non-controversial submissions by establishing that flamewars will not remain in high positions for long. (I realize that's a bit of a "broken windows theory".)