'Allege as a fact' means 'claim as a fact', or claim/assert that something is true although it is still unproven.
It is terminology used in law, rather than in general conversation.
"The witness alleges as a fact that you were at the site of the crime" means
The witness claims you were at the site of the crime. It is still unproven, but he states as fact that you were there.
IN THE CONFERRING OF HOLY ORDERS (It is 'holy', not 'holly')
A 'Holy order' is a Catholic sacrament/religious ritual performed by the church to enable a man to become a deacon, brother or bishop. A person is first 'conferred a holy order' if he wishes to become a deacon. Then another to become a priest, and the 3rd to become a bishop. Each of these holy orders is a sacrament or catholic religious ritual.