Tough spot Cr2sh. I appreciate people saying "it's not your decision, support your friend", but the friend in question has asked your to perform the ceremony and that makes this different. Personally, I don't think anyone who has the ability to perform a marriage ceremony should do so unless they feel good about the relationship. This is usually done in the form of "pre-marital" counseling. Either the officiant does the counseling themselves or a third party does the counseling and gives the officiant a report regarding how things went.
You could tell your friend that you won't do the ceremony until they get some premarital counseling. That way you've been able to express your concerns and even attempted to help them get off to a good start. If you are not comfortable with that or if they refuse then, like some other's have said, I would suggest you simply decline performing the ceremony and assume the role of a supportive friend at the event.
I was in a similar situation many years ago when a friend of mine got married. There were some fundamental differences between them that I thought were "deal breakers". He asked me to be a groomsmen in the wedding. At first I accepted, but then I later let him know that I couldn't do it. I didn't even attend the wedding. (Which I think was a mistake, I should have showed more support) The result was pretty much the end of our relationship as we didn't stay in contact after that. Years later he called me out of the blue to say that they were now divorced and that he should have listened to what I had shared with him before the wedding. He apologized for putting me in that position and said he respected that I was honest with him even though it was so difficult. Our lives have drifted apart and we don't stay in touch today, but it was an experience that taught me a lot.
True friends are supportive, but they also love you enough to confront you with hard truths. You can be supportive of your friend and his "wife" without having to compromise your own integrity. If they want to move forward despite obvious warning signs then that is their choice. You can be a friend and be supportive without having to be the one who says, "I now pronounce you husband and wife".
Edit:
One final point, after they are married they become a package deal. Don't every choose sides, put her down to him, or get in the middle. He chose her and you must respect his choice. Trying to be "his friend" while being critical of her after the wedding is dangerous territory.