If a Cylon Leader is Infiltrating and in the Brig, and the player chooses to go back to the Resurrection Ship, they have to discard down to 3 cards. As such, if a human player suspects that an Infiltrating Cylon Leader is working against the humans then putting them in the Brig is a good idea.
What happens when a Cylon Leader is executed? I assume they aren't treated as a human causing -1 Morale. If they are treated as a Cylon, the loss of a Super Crisis seems to have no real impact.