I sincerely doubt you won't be 'rewarded' for taking the other route. But none of us know. Just, play as you like and find out.
I also doubt it, but its not about getting a reward, its about balancing the game systems to be at least relatively fair for every type of playthrough. IMO good guys should get nearly as much gameplay as the bad guys. Also bad guys should get nearly as much story as the good guys. This is a balancing act of sorts. And the balance kinda shifted to the bad guys gameplay-wise.