With all of this information stored in the objects directory, you can safely delete the snapshot directory that you used as the source of this operation.
If you want to reconstitute the snapshot at a later date it’s simply a matter of following the SHA1 of the root tree stored in the message file and extracting each tree and blob into their corresponding directory and file.
For a single snapshot, this transformation process doesn’t get you much. You’ve basically just converted one filesystem into another and created a lot of work in the process.