I have just finished reading a comprehensive review on practical control measures against Salmonella in animal feed. This review, by Jones (2011, Journal of Applied Poultry Research, 20:102-113), clearly indicates that thermal treatment (usually pelleting) alone is not enough to eliminate Salmonella.
Additions of chemical products (such as certain organic acids and/or formaldehyde) are also recommended in combination or alone. Other measures are also proposed to (a) reduce the chances of Salmonella entering the feed plant, and (b) once unavoidably there, ways to reduce its multiplication rate.
I am sure this review will be of much interest not only to nutritionists, but also to feed plant managers!