I think reputation in Career mode is kinda backwards... If you ally with somebody, your reputation wont ever go below 0... which means, you can take all missions you want against your ally without problem and still have all benefits... so practically, you work for enemy, improve relations with them (to neutral)... but thats not how ally should behave...
I think it old system was a lot better - you do missions for a faction? more you do, better friends you are... You fight against faction? you become enemy...