Here's the report.
http://www.ntsb.gov/publictn/2004/AAR0404.pdf
The company didn't disagree that the FO used the rudders. The union investigator(s) didn't disagree that the FO used the rudders. Both of these parties had problems with the design and certification of the A300.
The union's crash investigative report detailed the design differences in rudder control. Only the newer Boeings (747/757/767/777) have the better design. Rudder travel is always the same, as is leg pressure. Other designs, 727/DC9/DC10/737/all Airbus models, have the system where rudder travel is reduced and the force required to get full deflection is reduced. The union's investigators pointed out that the A300 is significantly more sensitive than other designs.(NTSB agrees, page 146 of the report, pg 160 of the .pdf file)
At 250 kts the A300 rudder is 2X as sensitive as it as at 165 kts(most rudder applications x-wind, etc, are below this speed)(from NTSB report)
AAMP did not advocate large rudder inputs(several references to this in testimony, ie pg 86-pg100 of .pdf) (read NTSB report starting on page 80, pg 94 of .pdf).
Airbus stated the full use of controls may be necessary to control the a/c. And said to use alternating rudder inputs in the checklist for gear extension problems. It wasn't until AFTER the crash they published rudder recommendation in their FCOM manual.
Industry experts advised that all transport catagory a/c can generate loads, even below manuevering speed, that exceed design loads for rudder and stabilizer inputs. Caution is advised!