Part of the problem is...
...that a rather high percentage of the intemperate political commentary on the airwaves, in blogs, in letters to the editor, in the political literature sold in supermarkets, and on message boards; is associated with what used to be called the New Right. There is certainly equally intemperate commentary produced by leftists (especially the cultural left), and has been for decades (they're the biggest reason why the term "fascist" is now an almost meaningless insult), but at least in the USA, most has come from the right and that has been true since at least the mid 1990s (almost certainly associated with the rise of Rush Limbaugh and his many imitators). And a lot of Republican politicians and activists have come to see this sort of activity as an asset for their cause, and have therefore become extremely protective of it (even though small-c conservatives have traditionally put a high premium on aristocratic civility, and abhorred discourtesy in all forms).
And Mr. Smith may well be right that this project in particular is aimed specifically at right wing propaganda efforts while ignoring those on the left, but that's hard to say without examining it in a lot more detail than we see in this article. Given the huge amount of intemperate, malicious, and often irrelevant political speech infesting message boards, I think efforts, technological and otherwise, to keep discussions civil and on topic are completely proper, but I agree that such efforts need to be non-partisan and otherwise impartial. If this project indeed suffers from partisan political bias, then it shouldn't have been funded with taxpayer dollars; but there is a very good chance that Mr. Smith and like minded politicians protest too much. And in any case, any technology that can reliably be programmed to filter out right wing incivility and libel can be exended to filter out the left wing variety as well.
In any case, an insistance on civil discourse is not a restriction on free debate, but rather facilitiates it; as people are much more likely to state their true opinions and to discuss their reasons for them if they're not screamed at or defamed for doing so.
Disclaimer: My own political leanings are moderate to liberal (with conservative leanings on some subjects), so I may well be biased myself.