The problem of course is that by pointing to that site you are inadvertently promoting them. You and anyone other critics who point to the site are helping increase it's Google page ranking or Technorati authority. It does not matter, necessarily, if your site has low authority, others might pick up on this with a higher authority. So what can you do?
If it is a big news site there is not much to do, link direct.
If it is a site like the Discovery Institute I humbly suggest that you do not link direct but link to its Wikipedia article. The advantage is that you both do not promote the site directly and, by going through wikipedia you help promote that entry above the home website. The advantage of that is that since many users click on the first relevant entry they see they might be exposed to a more balanced view of the site under criticism - due to Wikipedia's Neutral Point of View Policy - although there may be ongoing debate on how neutral the article is, of course.
If it is a site that does not warrent an entry in wikipedia and you have found it via a blog, rather than just hat tip that blog who has a pointer to the site in question, link to them instead when referencing the site in question. If they brought the issue to your attention help promote them so they will be encouraged to do it again.
Of course, if you happen to be the first then by all means link to and criticise that page/blog/site on whatever basis you deem relevant. Hopefully others who pick up on this will link back to you.
These thoughts were triggered by me live blogging at the Weird Science meeting last Saturday. Not the my site has much authority it has been mostly dormant till recently, still I felt uncomfortable linking to sites under criticism by the speakers, especially since I largely agreed with the speakers.
Is this a good solution, are there better ones, or should I just link direct?