It seems like Larian does want to give us build and party flexibility, evidenced by having the built in respec as well as picking a class for each companion. However, when most of the companions you recruit are already level 2 or higher, you are faced with either having wasted civil points until respect much later, or picking a class that you don't really want to start as just to not gimp the civil points.
You're focusing on the symptom and not the cause. What would be better is for party members to NOT automatically allocate all their points from their level-ups after they join your party. Just give you the experience so they reach the level to match yours and let you allocate the points manually.
Right now I'm dealing with this by ignoring all sources of XP after waking up on the beach, then using the ladder to get into the fort and do all my recruiting before reaching level 2. This works for everyone except Ifan, though, as you can't recruit him until after somehow resolving the Shakedown quest, which gets you to level 2.
