Hello Flash,
It is denying that he would like to just go ahead and pardon Stone but he fears the bad PR. Despite having a very strong economy in which most Presidents would enjoy 70% approval polling and easy slam dunk reelection prospects. Highly questionable IMPOTUS can't even get a majority.
Saying it is "too soon" is not denying that at all. Very few presidential pardons happen immediately after a conviction--they usually come at the end of the year or the president's term. Presidents consider PR, how the public feels about the Stone conviction and sentence, etc.
I am not denying he may want to pardon Stone now but neither do you have any clue that he does want to do so. I would guess he will wait and pardon several of those involved at a later date.