Level 54 purple mainhand pistol still bolsters for more Primary and Bonus damage than Conqueror.
It's less of a boost than prior to this patch (now 23 more bonus damage approx over the Conqueror, whereas prior to 2.2.1 it was boosting for 70 or more damage.)
Haven't yet checked on the level 54 purple Rifle on my Vanguard to see if a similar reduction has occurred. Haven't checked implants either.
What is the expertise for each case? If the purple MH were to give you far less expertise damage boost and damage reduction then the Conqueror might still be better.
No PvE item should be better than the corresponding Partizan, much less Conqueror.