Lack of async operations in Workbench aside, using the internal IDE interface requires use of the CPU, and the filesystem process runs at priority 10.
If you really must be able to use some application or shell comfortably while such large copy is in progress, you can do it by raising the priority of the processes in question. Running them at priority 11 should help. Obviously this only works for the interactive processes, anything consuming tons of CPU time should not be adjusted.
BTW. Is 3.9 AsyncWB really stable? I remember talk of some nasty bugs in it.