Of course it will kill performance while it's running on a loop but that's why I said do it over night, and only until you have the problem fixed
Once you have sorted the initial problem out, the defrag only takes a couple of minutes at most to sort that days fragmentation out and stop it building to a point where you have to take the store off-line again.
It all depends on what sort of environment your in, but for me when virtually no one is using the system overnight a few minutes at lower performance is worth it to prevent future problems.
Also the original post referenced disk fragmentation only, so I not quite sure how we got on to exchange edb defrags. Checking for event ID 1221 will give you a good idea if there is any point to an offline defrag.
BTW Diskeeper V9, actively monitors the amount of disk IO on the drive it is defraging and backs down it's activity when there is other IO queuing for the drive, which helps maintain a decent level of IO.