There is one thing that actually really bothers me, though. Towards the start of the EA, it was said that Larian was only providing the evil companions at first to get feedback on them, basically making an assumption that they were going to be less popular options upon release.
The "neutral" characters are also included in early access, I found an interview with Sven Vincke that I had linked in some thread (I don't know where just now, but I can look it up). So I think there should be more than enough room for the "good" companions.
Personally, I am not worried that, for example, Helia has gotten the axe. I think that Larian might just be more careful with the data included in their patches, so that not everything is spoiled before full release.
But I think it would really help if the final number of possible companions would be announced in the next PFH, since many players seem to be worried about this.