From my understanding, a president has two options: he can pardon someone, meaning the whole conviction is removed and things like e.g. voting rights are restored; or he can commute a sentence, which lowers the penalty but upholds the original conviction. So, after being released from her commuted sentence, Manning will still be a convicted felon and traitor, probably won't be eligible to vote or stand for election, will never get security clearance, etc etc. Also emotionally, a pardon would acknowledge that what she did was (somewhat) right, while a commutation means that she is still guilty and her acts were wrong, just not deserving of such a hash treatment. This also sends quite a different message to would-be whistleblowers.
So, the difference between pardon and commutation is not a technicality, it is very real.