The answer lies in SilentHunterIII/Data/Cfg/basic.cfg
SH3 is scripted to subtract renown for sinking the wrong ship (neutral or friendly).
[RENOWN]
RenownReachGridObjCompleted=500
RenownPatrolGridObjCompleted=200
CompletedPatrol=100
NEUTRAL=-1
ALLIED=1
AXIS=-10
WrongShipSunk=-5000
FirstRankRenown=1000
SecondRankRenown=3500
EndCampaign=-5000
You
CAN edit that by removing the minus sign in front of the 1 for NEUTRAL.
Change it to:
NEUTRAL=1
Now you can sink anything but an AXIS ship without penalty. Not very realistic, but what the heck; those darn neutrals are sailing in the convoy and have to take their chances like anyone else.