I am about to graduate from university in England. One of the graduation ceremony traditions is to kneel on both knees in front of a seated master of ceremonies and place one's hands in between his in order to have the degree granted. There is also a ceremonial text which is usually the Christian "Trinitarian formula" ("in the name of the father, son and holy ghost") which I have agreed with the college to change for me to "in nomini Dei" alone. My question is, is the kneeling part also halachically problematic, and if so what would be appropriate to do? If you can provide sources that would be great - I want to understand the halachic context if possible. I am especially interested if someone else has been in a similar situation, what they did.
I can answer some of the question but not the real halachic bit.
This sounds just like the Cambridge graduation ceremony. It is quite common and I think officially accepted for people there who don't want to kneel to just go and stand and lean forwards instead. It may be common practice among Jewish students in your place to make use of this kind of exemption. Even if you conclude that the kneeling is permitted, backing the exemption for those who don't might be another consideration.
Personal experience: I have made use of this exception twice and know others who have, but not recently. A couple of other Cambridge graduation related points: you can mention that you don't want the trinitarian formula, but i think this only changes anything if you are the first in your ceremony/block. See here. If your procession leads to multiple ceremonies, you may be asked to wait in a church, you can easily hover outside instead.
(Another consideration when it was shabbat, because you exit the building straight into a public space: I asked my non-Jewish successor in the ceremony to take my certificate, and hovered inside the exit we leave from after graduating to give it to him/her. If there's someone more appropriate to look after it for you, you can transfer it from your successor to that person once everyone is together, back on senate house lawn.)
If there is a Jewish community around the university concerned, there's bound to be advice and suggestions available.