You only need to:
cleartool checkout -nc root_dir
cleartool rmname dir2
cleartool checkin root_dir
That remove the reference to dir2 in the new version of root_dir, making dir2 and all its content invisible (not reachable).
And you can easily restore dir2 (and all its content) by merging the previous version of root_dir (which was still referencing dir2) with the current version (the one where you rmname'd dir2) in order to recreate a new version where you get back dir2.
Note: when using rmname, you might have an error message mentioning that the element is in checked out, even though it is not checked out in the branch where you are doing the rmname.
using rmname -force is the solution to still perform the rmname: see this technote.