You can lessen the blow to -rep if you are good at persuading, for example if you accept a certain stone guy into the group when you have Allistair present, Allistair will go -10 rep.
If you [Persuade] Allistair its ok first, it wil be -3 rep, this works in other situations too.
On my player character i always go for coercion at max asap so i can influence everyone in rp situations and ofc for my companions awkward moments.
Another thing you can do if you have hindsight is KICK the person that wil object from the group first, such as a certain merchant in a certain village that tries to pay you to help him drive a woman away.
If you kick out Morrigan first, then side with the woman, after its over you can inv back Morrigan and her rep remains unaffected, lame but it works.
Best idea really is dont use Morrigan with Allistair or Wynne and your going to have a MUCH easier time of it ear ache wise, no idea who is gonna heal though ;P
Shale (tank) + You (dps) + Morrigan (Healer) + Random not Wynne, Allistair or Leilana is probably best (and more fun).
But id be willling to bet 98% of players use Allistair or Wynne or both every playthrough as they are the main non-PC tank and healer shame both clash with Morrigan though who is BY FAR the best NPC in the game. (she has 58% of the votes on bioware site lol)