Supervisor has said some very disgusting things online, should I pull my name from our paper?

No it sounds like the PI holds appalling views but no one will attribute those to you if you were merely his student. On the other hand those papers are valuable to you and hard to replace. Moreover the removal of your name from them may irritate your PI who, despite his antediluvian views, continue to be in a gatekeeping position in your field. We all have a responsibility to fight bigotry but that shouldn’t come at a cost to our most junior researchers — I suggest you pursue your careers whilst flagging his behaviour to those within and without the university who may be able to respond. Such a lecture would be sufficient to get you fired in many countries were it to be reported in a timely manner.

Should I pull my name from the papers at the last minute and lose accreditation for the hundreds of hours of work I put in, or do I leave my name in and risk having a reputation as “that guy who worked with the huge homophobe”

You have met a true moral dilemma in life, and it is a big one.

My recommendation is to first examine your own beliefs rather than what others may or may not think about you. See how important your principles are and act accordingly.

1. The martyr For those who value their principles above all, there is usually a price to pay. Jesus could have avoided the cross if he had backed down. Gandhi and his followers went unarmed against oppressors who were armed with clubs and received the expected bruises. Such a person is rare. In your case it would involved refusing to "consort with the devil" and simply being prepared to forfeit your hundreds of hours of work. You should also bear in mind that the other party may believe in their principles to a similar extent - rightly or wrongly. Thus have religious wars been started throughout history.

2. The human approach You can consider humans as fallible and usually flawed. You can try to understand where they are coming from and even sympathise where necessary. Often when people are vehement and angry, they are reliving a past battle, maybe a trauma that remains unresolved. As a student hitch-hiker, I was once subject to an attempted assault by a gay man; luckily I escaped unharmed. In my case this did not turn me against gay men because I already had gay friends who were admirable people in every respect. Instead it made me much more careful about hitch-hiking! Had I been younger and not known better, it might have been the start of a prejudice.

3. The pragmatic Here you look at outcomes, assess probabilities and make the best decision you can. To go this way you must be very clear what you want out of life. If you don't know the desired destination, you can't find the best method to get there. "Best" doesn't necessarily just mean short-term academic goals.

4. The Machiavellian In this case you take sides and strive to come out on top. For example you could denounce the 'opponent', let public opinion do the dirty work, and at the same time declare your own virtue. When they are destroyed and retreat, you take the field, the spoils of war and the glory. However, unless you are very skilled this can backfire. Suppose the other person is not destroyed. What do you do then? Pretend that you didn't mean it and go back to co-operating? This will only show that your principles are not so true as you made out.

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Life is a tricky business. I wish you all the best. Remember what Nietzsche wrote, “Out of life’s school of war—what doesn’t kill me, makes me stronger.” I'm retired now and have learned to believe it.

So many people are waiting for things to "turn out right". I believe it is better to see life as a series of challenges to be met, and to meet them. This can actually make life great fun but you have to take risks.

Consider how removing your name from the paper affects You and how removing your name affects the PI (Principal Investigator).

"I'll shoot myself in the foot, that will fix him!".

It's not the responsibility of (relative) beginners in the field to reform the personal habits of researchers in the field. You could do more pre- investigation of future employers, if you like.

Science is about discovering. Even A**holes can discover.

The other answers here (at the moment: Well..., Arno, and Libor) give good advice that it is unnecessary for you to withdraw from the paper in most cases.

But there is an exception to this. If the nature of the research is such that the misinformed opinions of this person can affect the results, then you can have little confidence that the overall result is valid. And since you were mostly involved with technical issues, not the driving ideas of the paper, you should consider this.

There have been people in both CS, William Shockley, and mathematics, Robert Lee Moore, who held terribly racist views, but whose scientific work was independent of those views. In a case like that you should almost certainly leave your name, since the work is done. But I would probably disassociate myself from them in future.

But if the field is closely related to those views, then it is much more problematic to be associated with them. But it is the views that you need to disassociate from, not necessarily the person. (But who needs the grief?) You don't have a choice in your crazy uncles, but you do have a choice in your colleagues.

FWIW I worked professionally with one of the guys at Stanford who now has strong, shitty opinions that he feels twitter MUST know. The only blowback I've ever had was people chuckling about how he's gone off the deep end, and I was much more senior than you currently are.

The idea that academia will punish you for wrong opinions is mostly nonsense. If you aren't loudly bigoted about people your job requires you to interact with you'll be fine (like any job). Just make sure you aren't his TA or something when he goes on some insane rant and try to find a mentor who didn't lose their mind.

While I strongly feel that people like this should be ostracized, I think the onus is on their instituations and peers - not on undergraduates. Very few people would blame you for having worked with your supervisor, and should you ever be accosted for it, you can truthfully point out that you embarked on the research internship before learning of his repugnant views.

From a purely pragmatic perspective, having this conference paper on your CV will do more than enough for your grad school applications to outweigh the risk of your reputation being tarnished by association here.

If you feel that you need to do something about the situation, my suggestion would be to signal your own views in other ways. For example, if your university has something like a gay-straight-student alliance, volunteering there and putting this on your CV should get you ahead of any unfortunate associations. Again, I don't think you need to do anything, neither from an ethical nor pragmative perspective.