For the most part you are correct, except that there is one option that I didn't see you mention in your post:
Embrace the fact that there is no channel to channel isolation, and
reference both inputs to the same ground. So, you would only need to
use one current source for all thermistors, and tie them all together
in series. Then on a single SCC-AI module you could reference Ch0 and
Ch1 to the ground of one of the thermistors, but since they are in
series the voltage on the second thermistor with reference to the first
thermistor is equivalent to adding them up. So, one channel will read
the values that you expect, and the other channel will read the
equivalent of Ch1 + Ch2. So, as long as you know the value of Ch2, then
you can compute Ch1 by subtracting Ch2 from your readings. This will
double your input range, so you won't be able to apply as much gain to
your measurements, but it will still work.
Also, for the filtering, you could cascade the output of the SCC-AI modules to the input of a SCC-LP filter module:
http://digital.ni.com/public.nsf/websearch/7B801B3C9E0B82A386256C25007640CA?OpenDocument
Regards,
Logan K