I had a lot of issues with Scully's characterization in Iolokus (and with Mulder's as well, but not to the same extent). I mean, I love the story but I had to completely separate my version of M&S from theirs. I think as the story went on, I could put aside my initial dislike of Scully for the most part, but it was not an easy read for me. I haven't read it in a long time, so maybe my opinion would be different these days.

So while they are both somewhat out of character here, it's more believable for me considering their world has just been rocked by the destruction of their office (and as amyhit says below) and of The Work.