It shouldnt if they can communicate and really respect each others view points, even if they disagree with them. They will have to make certain practical decisions like sending their children to Frum schools and come to an agreement as to how they act in front of the children and or in public where it will affect the children. If they can do this (and I believe many can) then they will be fine. If they agree on what to do practically why is it any different then disagreeing on what constitutes good music or food etc.
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