If you mean agree as in "agree to coexist," yeah.
If you mean agree as in "agree with each other's arguments," I'd say no, it's not possible.
I don't understand what you mean by saying that the conflict hurts both parties. I mean, look at politics. Democrats and Republicans don't always agree, but nobody thinks Democracy is stupid because the political parties don't see eye to eye.
Saying that disagreements about what kind of God there is weakens the idea that God exists is like saying that disagreements about what kind of Foreign Policy the US should pursue undermines the idea that we should have a foreign policy of some kind.
Ultimately, though, you get two groups who are trying to uphold what they see as the most important thing in the universe. Obviously, when that much is at stake, compromise is difficult.