Total number of comments and clicks on the articles would be the metric. Time spent on site would be a great measure too.
Using two of my own submissions...
Compare Google's blog post on robots crawling news articles: http://news.ycombinator.com/item?id=708417 to an inflammatory post about Techcrunch: http://news.ycombinator.com/item?id=658308
One of those is 'quality', and the other has comments (and 'dead' status).
It doesn't meassure the quality of the discussion and the submissions.
I simply suspect that the 'points' system has a shadow side and that as the site grows the shadow side starts to overpower the positive portion. By temporarily switching it off and asking the community what they felt about being 'point blind' for a short period and if they thought the quality improved or not you can make a 'metric' that is much easier to measure than some of the more technical tricks you could pull:
Customer Satisfaction.
If on average more people feel better without the points visible than with them after a short trial period then it's something that you could consider doing permanently.
Another option would be to keep author and points hidden until after you've voted for a comment, but that may have other side effects.
I think the content should stand on its own, regardless of what the voting history and the author are it is what you think about it that counts.
Right now the choice to vote or not to vote is made plenty of time based on the current number of votes, which leads to plenty of feedback loops. I've seen 'flip-flops' (bi stable and tri-stable, 0,1 and -1,0,1), positive feedback loops, and negative feedback loops.
By breaking the loop we could end up with a more balanced view.
Imagine what the effect would be of a running tally during an election, it would completely affect the outcome, and not necessarily in a positive way.
Again, it's just a gut feeling but I think there is some truth to it, and it's a very easy to do experiment, worst case we will learn that it did not work.
I think the experiment would be a great idea and doing it the way you propose with empirical data to back up the machine generated statistics could provide very valuable insights.
Also one could start experimenting with the approach/idea e.g. let the number of votes appear after voting or not displaying a number at all
Regarding clicks, I think even if people just click every comment link to find out what the discussion is about, the site/design has achieved its goal. It may reveal whether the points cloud new interesting articles.
Perhaps, this experiment could also include clouding of domain to see if techcrunch and other popular domains get extra juice thanks to its popularity.
That said, you can (and should) measure performance on multiple benchmarks like clicks, comments, time spent. Gives you a correct picture of tradeoffs.
If you only test one variable at the time then you simplify your tests to the point where you can extract some metric to determine whether you've improved or not compared to the old situation.
Nothing stops you from then doing more ab testing with other combinations relative to your 'new best'. This may include going back to the original setting with some other variable changed, that way you avoid the local maximum problem.
So say we have a site in position 'A', we make version 'B' and we test them against each other. If we find out according to our chosen metric that 'B' performs better we now have several choices:
We can do another A/B test starting from 'B' changing some value to see if we can improve on 'B' directly, or alternatively we can go back to 'B' versus 'A' + some new modification that is not 'B'.
I hope that's clear....