I actually like this blessing idea. I think if you are already at 100%, you should go a bit higher or prevent the likeliness of your men ditching the field from panic would also be a nice way to go if you don't want to touch the morale part.
Also, units should go with their lord's religion. If they are blessed by a religion that your noble is not a part of, then you should lose morale instead. Or giving a chance of priest getting beaten up.
As for pagans, they won't benefit at all.