Not knowing all defraggers funnies, I'd not recommend as BOINC and the defragger might grab the some file for writing i.e. risk of corruption. If you want to try, exclude the BOINC program and data directory structure. Those files are highly volatile anyhow, so what's the point of defragging them.

In summary, exit BOINC altogether for the safest route.

I've done both but usually only pause Boinc on slower machines and older OS's (i.e. Win ME/98) because Defrag is slowed down to a crawl and usually have to shut down nearly all running programs so that Defrag can finish in a reasonable time. Win XP defrag works OK. This defrag problem doesn't exist with Linux as far as I know.