Is Assassins Creed II sacrilegious

In some ways, yes.

There are several missions where high ranking church members are actually Templars (bad guys) and often want power or the death of others, which is against all christian teaching.

It also imposes a brand new creation story, involving many god-like beings, showing remarkable resemblance to the 4th Indiana Jones movie.

There are also holy artifacts that kill people and are addictive to wield because of the power they give you. (The pieces of Eden.)

So, to be blunt, I'd say it is.