I read a quote from the actress saying she hopes they don't go Peter/Olivia, because "that would be so conventional." But when I see these episodes, I think, OMG, how could they NOT go there? They have totally smokin' chemistry together.
And she's not the first actress to say that about a ship her character is involved in. I think for some actresses there's a fear that they would get relegated to 'the girlfriend' or something. However, at least where Alias was concerned (I've never watched Lost) JJ has a pretty good track record when it comes to 1) following through on UST and 2) keeping the female lead completely kickass.

At this point in the show, though, I think the focus is still on Peter-Walter and Olivia-mytharc. Which I'm okay with because both equations are keeping my interest... although lately the eps seem to be straying away from the mytharc which is too bad.