First of all, and this is something you never hear about, the Pioneer anomaly was also shown by another spacecraft: the Ulysses spacecraft which was launched, via a gravity assist at Jupiter, into an orbit around the Sun out of the plane of the ecliptic. The Ulysses orbit could only be explained, said Anderson et al. (1998) (see ref below, page 2) if they included an unexpected acceleration of 12+/-3x10^-10 m/s^2 towards the Sun, in agreement with the Pioneer anomaly of 8.74+/-1.33x10^-10 m/s^2. The Ulysses spacecraft had a different orientation to the Pioneer craft so it's very unlikely thermal emission would apply in the same way.
This supports my opinion that the Pioneer anomaly has been brushed under the carpet by a complex thermal model (that has 1000s of finite elements and two adjustable parameters) rather like the galaxy rotation anomaly has been brushed under the carpet using vague and complex dark matter models. Uncomfortable contrary data like the Ulysses data in the case of Pioneer, or dwarf galaxies in the case of dark matter, have been hidden away in a dark closet like a grumbling relative with a higher standard of cleanliness, but they are still there, muffled but more determined than ever to expose sloppy practices.
Going further, the Pioneer anomaly is not only supported as an anomaly, to the standard model, by the Ulysses data, but also by the galaxy rotation anomaly, the anomalous cosmic acceleration, the flyby anomalies, dwarf galaxies, the Tajmar effect, the emdrive and many more, all of which are easily solved by the same acceleration shown by the Pioneer craft, an acceleration that appears naturally within the framework of MiHsC (see my papers below for the solutions for the Pioneer, galactic and cosmic acceleration).
The fact that the same number 2(SpeedofLight)^2/(HubbleScale) ~ 8x10^-10 m/s^2 keeps cropping up all over the place, should really get massive attention. This is direct evidence for MiHsC, because only MiHsC predicts that crucial number (even in MoND for example this odd number has to be put in by hand).
ReferencesAnderson et al., 1998. Indication from Pioneer