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Generally speaking you should be OK...unless it's something super critical. Also having a monitor with focus assist can help. 5D might be known for super shallow DOF but if you can close it down a stop or two and balance things out a bit more. The less critical the shot in terms of shallow DOF, the better off you'll be.
Everybody who has the 5D has to deal with this in some capacity, so you'll be just fine.