You've described quite a few conditions in your initial post and so I don't think it would be possible to address them all in one comment.
However... in a nutshell, the general idea, when shooting raw is to shoot with as low ISO as possible(whenever possible) and work with the files afterward.
However, as you yourself may have noticed, there are so many factors that can come into play, that it may seem impossible to address them all.
Though one simple formular, is to aim for as high as shutter speed as possible whilst maintaining as low an ISO sensitivity as possible - confused yet?
Anyways, on the issue of noise, I think you've hit it on the nail.
And that is where we'd shoot RAW and deal with noise in post processing(development stages) afterward.
And with today's tools(Adobe Camera Raw or Lightroom), there is little that can't be negotiated in terms of noise reduction.
And things only seem to get better with every developing version of software we see. And so RAW seems to be a very good investment.
PS. I've seen ISO51200 from the K-5 that can were every-bit as impressive as ISO3200 ones
K-5, RAW/DNG, RPP, Topaz Denoise 5, ISO51200 Image courtesy of dgais