If you try to take the complement of the edge set to translate a max cut problem, you end up not minimizing cuts, but cuts minus a correction factor that depends on the size of the subsets in the partition (namely, it is the product of the sizes). This changes the nature of the problem considerably - if you have a dense graph, min cut will tend to separate a small chunk, while the corrected version will not.
Edit: A previous version complained about a difference in input type, hence David's comment.
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