You can definitely get pardoned before getting convicted. Trump pardoned Stephen Bannon after he got indicted wire fraud and money laundering, so he never went to trial for that.
He is getting a conviction. This is a plea deal. He will be admitting to the crime of conspiracy after which he will be a convicted by the court. He will then be a convicted felon and could be pardoned, but I doubt that is really an option. (Not 100% on the felony thing, I haven't seen how this is being charged.)