There's debate whether Trump could pardon Manafort. Depends on what charges he gets apparently. And even if he does accept the pardon it just means that he can't refuse to answer question about the crime that he now admitted doing.
Trump can go ahead and pardon Manafort if he wants; the guy's still going to jail. Mueller made sure of that. Check out the terms of the plea bargain Manafort agreed to; part of it required pleading guilty to all crimes. Not just federal, but also state crimes in multiple states (off the top of my head, I know New Jersey and California are included). Trump can't pardon those.
And notice that Mueller waited until AFTER Donnie Dumbass submitted his written responses to Mueller's questions to reveal that he knew Manafort was lying the whole time? It's been reported that Manafort was also reporting to Trump's lawyers... What do you think the odds are that Mueller fed Manafort bullshit information for a few months, and waited for Donnie Dumbass to respond based on that bullshit information?