Yes, efforts were made in Complex Traits to balance for all options, including pure and no negative. No negative does have a few more balance factor issues in spots than most options introduce but they should still be minor enough to just mean a few traits aren't QUITE as valuable as others, perhaps not even to a noticeable extent still. TBH, not playing with Religious Disabling probably creates the greatest imbalance issues in Complex Traits but that can't be helped because it's either a trait has or doesn't have the ability to adjust the religious building behaviors and there isn't really an in-between on that. It just means that without that option, some traits aren't QUITE as valuable or penalizing as they normally are, but then again that doesn't keep those from being valuable enough to want or want to avoid, so it isn't THAT big a deal. You don't HAVE to play with Developing Leaders, but the gameplay should be a little smoother in terms of early game balance if you do.