I suppose it depends on the nature and cause of the knee pain, and it would be best to determine that first.
Ifthe knee pain is somehow related to your posture or pelvic alignment, for instance, then it is possible that pilates could help as it seems to improve posture and to improve the strength of postural muscles that may not be activated or used much without doing exercises specifically designed to do so.
But I'd suggest determining the cause of the pain first, if not known, and take it from there. If the pain is due to some tendon, muscle or postural problem then my bet would be that specific stretches or exercises prescribed by a physio could be more effective. While my pilates classes involve ITB stretches, there aren't many other exercises that focus on such things specifically, though there are lots of variants of lunges and what not that presumably improve stability.
I'm still going to my pilates classes, 2 or 3 times a week - that's nearly 9 months now which is pretty good for me. I've no doubt that it has improved things on the back, er, front (touches wood), and I haven't injured myself or got bored with it. Even after all those classes, almost every class includes some move that I haven't done before. This is reformer-based pilates and the possibilities seem endless.