In order to have the thugs disabled, you have to visit the exterior before reporting to the questgiver. It can be fixed in the following way:

1. add a global variable TR_m3_AT_TG_Q6_ThugsDisable
2. in TR_m3_AT_TG_Q6_Thugs_sc, delete the conditional branch elseif ( getJournalIndex TR_m3_TG_AT_Q6 == 140 )
3. at the top of the same script, change if ( control == 1 ) to if ( TR_m3_AT_TG_Q6_ThugsDisable == 1 )
4. in the dialogue entry in "Camonna Tong's ledger" topic by Andor Orothi, which updates journal to 140, add set TR_m3_AT_TG_Q6_ThugsDisable to 1