There are a lot of personal dynamics that are difficult to accept outside of swallowing the "they're all cast members" pill. The good thing that the writers do is mention that there are other missions we don't see, which means there's always room for development happening off screen.

So, for example, we know there are at least two missions between "The Enemy Within" and "Emancipation." On one of those missions (or in the down time between), Daniel could have had a talk with Teal'c, or Jack could have stepped in (anticipating that Daniel might eventually leap to the conclusion that Teal'c chose Sha're). But having what is likely 2 or 3 weeks between those episodes means that we have enough time to get them into a good working relationship so that by the time "The Broca Divide" rolls around, I can assume that Daniel and Teal'c are actually finding common ground and developing a working relationship.

Another thing to consider is that Daniel FORGETS ABOUT SHA'RE ALL THE TIME. Like, I love him and it's very clear that he loves and cares about Sha're, but he also gets really caught up in studying cultures and crystals and not giving a single thought to the fact that those things are not hunting down Apophis. He is easily distractible. So it's honestly very possible that he didn't make the connection that Teal'c chose Sha're until like, "Bloodlines" when he's confronted by the fact that Teal'c was First Prime and maybe that goes into his passionate decision to kill all the larval goa'uld.

... I did not expect to spew that many thoughts about this topic.