Schmidt, Shindell and Harder (2004) argue that it may be possible to explain the changes Ruddiman was talking about through natural variations (including feedback responses to such variations), and that the data isn't good enough to exclude that possibility. They do not claim to disprove Ruddiman's hypothesis, merely that the evidence isn't strong enough (as at 2004) to accept it.
Joos et. al. (2004) find that Ruddiman's hypothesis would require a larger decrease in the atmospheric ratio of two (stable) carbon isotopes (13C:12C) than is observed in ice core data (methane has a lower ratio than the atmosphere at large, so large releases of methane would decrease the ratio in the whole atmosphere). They estimate that changes in land use around the time probably caused a 4-6ppm rise in CO2 levels, compared to a Ruddiman's 2003 estimate of 40ppm.
Clausen et. al. (2005) take a rather nuanced view, but, while they have several issues with Ruddiman's hypothesis, and its incompatibility with Joos et. al.'s results, they acknowledge that Ruddiman has a point, and that natural variation isn't sufficient to explain pre-industrial changes observed.
More recently, Kaplan et. al. (2010) pointed out that many lines of evidence suggest that the assumptions of constant land use per capita cannot be supported, and so can revise previous estimates upwards, figuring that anthropogenic emissions contributed a 7ppm rise in CO2 levels by 1000BC, and around 22ppm by 1850AD, and that these were sufficient to alter the climate (but not necessarily enough to prevent an ice age).
In 2005, Gavin Schmidt (a top climate scientist, and coauthor of one the papers I mentioned earlier) identified the hypothesis as one causing genuine debate in the scientific community. Meanwhile, Real Climate (a blog coauthored by several top climate scientists, including Schmidt) has offered Ruddiman several opportunities to expound on his hypothesis [1, 2], most recently less than a month ago, suggesting that they see it as a legitimate question.
It does seem that pre-industrial human actions were sufficient to alter the climate to some extent. Most recent results have suggested that this impact was less than originally estimated by Ruddiman, but sufficient to have a notable impact on the climate. Whether they were enough to prevent an ice age? Probably not, but not out of the question.
Meanwhile, Ruddiman does seem to have kicked off a very productive area of enquiry into pre-industrial anthropogenic climate changes. This does seem to be something that more sophisticated modelling and better paleoclimate data will reveal more information on in the future.