I think this denial helps everyone. The Russians can say they are not a threat, while the fact that the Russians are “upset” by it (which they really are not), show that Trump is not aligned with Putin (which he really is). A win-win all around (except for Hillary, lol).
Yeah, if the news cycle is Trump standing up to Putin (with a barking hillary ad no less) it elevates Trump to the world stage and leaves the wannabees behind.