A NASA team recently (july 2011) doubled the amount of available data related to the pioneer anomaly, and they saw an exponentially decreasing acceleration with a 27 year half life, consistent with the thermal scenario. More precisely they say :
The rationale for an exponential model is based on the possibility that the acceleration may be due to thermal recoil forces generated on-board. Due to degradation of the RTG thermocouples and changes in the thermal louver system, the resulting thermal recoil force could have a half-life significantly shorter than the 87.74 year
half-life of the ²³⁸Pu fuel, with 27 years being in the acceptable range.
For them "The most likely cause of the Pioneer anomaly
is the anisotropic emission of on-board heat" and promise a more detailed analysis.
The paper is arXiv:1107.2886 (now published in PRL) and there is a short discussion on it on The Physics arXiv Blog.
From my (scientist but non-expert) point of view, this temporal decay looks like an independent confirmation of the thermal origin of the Pioneer anomaly and basically settles the question.
Edit (2012-04-20): The same team just published arXiv:1204.2507 another confirmation, based on a detailed modelling of the thermal radiation of the spacecrafts. The last sentences of their abstract says:
As a novel element of our investigation, we develop a parameterized model for the thermal recoil force and estimate the coefficients of this model independently from navigational Doppler data. We find no statistically significant difference between the two estimates and conclude that once the thermal recoil force is properly accounted for, no anomalous acceleration remains.