I remember this scene quite well because it was very awkwardly shot.
IIRC, Will placed a cross in the top of the coffin, so that when the coffin was closed the cross would face down towards Barnabas. Personally, I don't think it would've affected Barnabas at all. He could've just closed the lid or turned away like he did when someone would hold a cross up to him.
The reason that Will moved around the coffin and off to the other side of the set was so that they could get the camera angle that they needed. You see, IIRC, they later showed Barnabas laying in the coffin and Will closing the lid, after Will's little aside to the camera. So, Will moved off to the side to allow for the cameraman to zoom up to him while he was talking and cut Barnabas and the coffin our of the frame so that Jon Frid could climb into the coffin without being noticeably clumsy.