Is there a way to turn off logging of every single timestep? I would like to redirect boinc logs to a file, but cpdn produces > 2MB a day.

Unfortunately not, you could direct everything to /dev/null and important messages from BOINC will be in the boinc stdout/err.txt. If you want to track your model progress the trickles should appear on the website soon after every 10802 timesteps. Or run the ./viz program?

I'm a bit late, i know ;-)
So, how about using grep, like
./boinc_4.09_i686-pc-linux-gnu|egrep -v ' - PH [1-3] TS [0-9]{6} - '>>boinc.log
this should filter out any Timestamp-logging and append any other output to boinc.log