I've heard it's great at all flows above 1500cfs. I've only ran it at high water, 20,000cfs. It has completely different character at various flows, and if you go low, plan on a long day. Good news is it has been running between 3k and 5k for a month. I just watched a video of some friends that went in there this past weekend. Looked like a lot of fun.
You are correct that it no longer runs year round. Much of the year it is nearly dry as I think they use some of the water for irrigation.
If it's high water (above 15k) go look upstream at the Milner Mile, what Rob Lesser describes as "the biggest big water in Idaho." It's four minutes of madness, and only run by expert kayakers. At this flow expert kayakers continue downstream and run the 25-30 footer known as Star Falls (or Cauldron Linn) on the FAR LEFT channel as the right channel drops into a certain death hole. Below here you have two large awesome rapids and then the start of the Murtaugh section.
At low water (below 2500cfs) I hear there are some exceptional play spots on the Murtaugh. Optimal flows would probably be between 3k and 8k if you are wanting the easiest of flows.
If you have the opportunity to go in the coming days, I would recommend it as it rarely runs this time of year.
if you have a facebook account, check Login | Facebook
to see my photos of the Milner Mile and Star Falls (the few miles directly upstream of the Murtaugh which runs at high water)