Initially all tools for survival are by-products, so of course the to ideas are not mutually exclusive.
I tend to think that the by-product theories are more true insofar as religion is hardwired. That's because the elements of religion that help people to survive depend heavily on the environment, thus the differences in religions.
Most of the things that are considered advantageous about religion are more arguments for basic human social adaptations: cohesiveness, etc. They do not require religion to work, merely socialization. What seperates religion from other types of behavior is the emphasis on the supernatural and on ritual (which in a way is kind of a primitive "science").
The other elements that are considered to be useful of religion or at least were in a more dangerous time seem more true of tribalism... And such developments aren't necessarily beneficial today.
I tend to go with Stark's exchange theories about religious social evolution. Religion is most beneficial in how it aids the individual. So the main thing I agree with the adaptationists on is that religion does help us to stop worrying about things that are unexplainable and get on to more immediate concerns. Of course in modern times we have plenty of time to contemplate the mysteries of the universe.

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"It's never over... BOY!"
The Tall Man, Phantasm III