It's just the basic problem of reboots that fuck with the originals. THAT "confuses the general audience".
No.
If people can keep track of all the reboots/restarts in the comic-book universes, they will have no problem with two versions of Star Trek.
Yeah, the two timelines are different enough that they won't be confused. Now, there are folks who aren't too familiar with Star Trek, and they might be a bit confused (understandable, of course), but most folks should get it okay, or at the least, a little exposition will take care of that.
Yeah, I think my wife is in that latter group. Like she doesn't care enough to make distinctions about alternate timelines or different stories. I just had to explain that these two new movies are a reboot like how the new Batman movies are a reboot.
And I know that we feel like that's a small percentage of people, but I think that's because we're people posting on a message board with other people who are just a bit more hardcore. I saw several people walking out of the theater explaining things to their confused looking wives, and it was somewhat amusing.
And I've seen similar things crop up several times before with something like Terminator, which has had it's share of alternate timeline style reboots. People come around asking the same questions like, "Where is John's wife Kate?" Or, "What happened to the Terminator played by Summer Glau?" Because they only peripherally pay attention. I feel that these people are more common than we think.