Having taken both the J! qualification quiz, and the Millionaire quiz, I can say that the J! quiz is definitely tougher, for two reasons:
1. Millionaire is multiple choice, J! is fill in the blanks;
2. Virtually all of the Millionaire quiz questions are $32K and less questions taken from previous shows. If you've been a regular viewer of the show, you will have been exposed to all the answers at some point. This would make passing the quiz a lot easier, but doesn't necessarily indicate whether you'd be any good at answering actual questions on the show where you haven't seen the answer before.
As far as the point that Millionaire is tougher because one wrong answer and you're out, I have to disagree. First, it's multiple choice, so the right answer is in front of you. Second, you don't have two other people trying to buzz in ahead of you, so time isn't a factor. Third, you have the option to walk away with the money you've won and not answer the question. Fourth, if you hit a plateau, you're guaranteed at least that much money, which gives you a safety net for guessing the $2K and $64K questions. And finally, you do have lifelines, so you're not without help.
Millionaire's producers may well have decided to trade off contestant skill for their TVQ value. It's not clear to me that the two are mutually exclusive (see the ratings for the initial runs of Millionaire for proof of that), but it's their judgement call to make, as much as I might disagree with it.