I was there at the end of '01 when the Maoist action really started to gather momentum. The biggest risk to your trip is travel disruption. I got caught in a general strike on the day I needed to head to the Indian border to catch a train in Gorakhpur. If you are happy to fly in to KTM, fly on to Pokhara and trek from there you would have a reasonable chance of a disruption free holiday. Anything else might get complex.
I am looking forward to going back one day - I have fond memories of Patan in particular.