Is there any reason to feel guilty if a chosson wants his Rosh Yesiva/Rav/Rebbe to be Mesader Kiddushin vs. his parents who want a relative who has semicha to be Mesader Kiddushin? I realize that according to halacha it is preferable that the Mesader Kiddushin know the halachos of Gittin and kiddushin and, therefore; the Rosh Yeshiva is far more qualified than someone who just has semicha. But, it can be argued that in practice we see even one who hasn’t learned those halachos be Mesader Kiddushin. There is also an issue that the chosson has, in reality, a closer relationship with his Rav than he has with the relative .This can cause tension if parents don’t understand these halachic and emotional issues.
It is understandable that the chosson would want that his Rosh Yeshiva or Rov should be the mesader kedushin, besides that he is also more qualified. However on the other hand, it is also important not to fight with your parents, and that you take their feelings into consideration. This is especially if they don’t understand the halachic issues involved and because they might resent the fact that their relative not getting the honor even after the chasuna. It is important to try to keep things as peaceful as possible.
I would suggest, if possible, that you speak to your Rosh Yeshiva about it, and important points you have to know for the chuppah, and write the kesubah with him beforehand, to make sure that it is written correctly, (spelling of names or any other kesubah issues that might be of importance). If you are afraid that the relative will be insulted by this, you can have the already written kesubah printed nicely, or written with calligraphy, so it won’t look like you went to someone else. You can also ask the mesader kedushin to attend the chuppah, (and of course give him a nice kibbud) so he can be on hand to see what is going on. This way you will be able to keep the peace, and have your needs and your parents sensitivity cared for.
May HKB”H send you much shalom and nachas in your new marriage, and you should be zoche to build a bayis neeman b’yisroel.