This is actually a question that's come up in my family, since we too have a number of religious faiths in the various branches (from pagan, to devoted roman catholic, to reformed but kosher observing jewish, to buddhist, to devoted athiest, etc). And with a lot of young children bouncing around the subject of selecting guardians has been done to death.
My feeling is that any family member who selected DH and I as guardians would be more or less ok with the fact that we are Pagan Unitarian Universalists. We would do our best to ensure that their children were raised in and familiar with the tenents of their parent's faith, but our own family would remain pagan unitarians and that would influence a lot of our day to day activity. So, for example, if my jewish cousin passed away and left her children to my care, I would meet with the local rabbi and do my best to ensure that they were adopted into and supported by the local jewish community. But I wouldn't keep a completely
kosher kitchen the way my cousin does (with two sinks, two fridges, two stoves, etc) and her children would accompany us to UU or pagan rituals simply because that is "what we do".
Likewise, when DH and I were trying to figure out who would take custody of our own children in the event of accident, we didn't consider relations who have belief systems we disagree with. We finally asked family members who have a similar religious background to be the primary caretakers (they are asatru), and family members who have a different but not antagonistic belief system (agnostic, raised unitarian) to be the "backup" caretakers. But knowing their personal religious convictions played a part in who we selected... basically, we picked people we thought would be the best parents possible to our little ones, and religion was part of that "best parent" package. We don't assume our kiddos would be raised exactly the way we would do it (up to and including religion) but we do expect that these guardians would honor our wishes to the extent practical and make sure our children were familiar with paganism/unitarian universalism.
But one way or the other, it's a decision made after many discussions between parents and between the parents and the potential caretakers, so hopefully this would be discussed honestly (and then never needed).