Conflict may not be pleasant, but raising your child and supporting your spouse is your responsibility. It's not something you can avoid just because you don't want to rock the boat. That's why your spouse must remain by your side — confronting family members is much easier when you have strong emotional and psychological support.
What you say and do will depend upon how aggressive the family members are. Are they teaching her things that are contrary to what you are teaching her? Are they actively and aggressively evangelizing her, trying to get her to commit herself to their belief system? That has to stop, and immediately — perhaps it would be acceptable for them to "share" their beliefs if that simply constitutes explaining what those beliefs are, but active attempts to convert crosses an important line.
Unfortunately, some may not recognize the difference between "sharing" and evangelizing — if you can't explain it and/or they cannot hold to it, then it may be unwise for you to leave your child alone in their care. That may sound harsh, but it isn't acceptable for them to undermine how you raise your children.
Are they doing things behind your back, like taking her to church services even after you asked them not to and then telling your child to keep it a secret from you? Are they giving her religious icons and telling her to hide them from you? That also has to stop immediately — teaching your child that it's OK to lie to you and do things behind your back is just plain wrong, and the "noble" intentions of teaching her religion utterly fail as a justification. Once again, perhaps it wouldn't be wise to leave you children alone with such family members.
Are they giving her religious gifts — for example, a children's Bible? Some gifts you may not want her to have, but others may be useful teaching tools. You can use them to help her understand what others believe — just so she understands that just because something is portrayed as a fact doesn't mean that it really is a fact. So long as you have the opportunity to approve of the gifts before hand and talk about them with your child later on, there shouldn't be much of a problem.
Are they saying grace before dinner? Whether they say grace is their own business and so long as your child is not expected to do anything more than sit quietly and respectfully, there's nothing to complain about — although at some point you may want to talk to her later and explain why some people do that. However, if they expect her to participate even though she doesn't share or even understand their beliefs, that's crossing over the line.
Whatever the circumstances, you will have to sit down and have a frank, open discussion with your respective families about how you intend to raise your children and what you intend to do with regards to religion and theism — preferably before you actually have kids and therefore long before any conflicts become immediate. You need to emphasize that how you raise your children is ultimately up to you and that you won't tolerate interference by others when it comes to religious matters. Be gentle and be kind, for this is your family; but be firm as well.
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