A couple of points to toss into the discussion here:
1) Wetlands are very important in controlling floods through the storage of water. However, most of our understanding of how wetlands work in terms of flood control is in the context of open systems, or in other words, a typical stream system. Devils Lake is a closed basin system. Eventually, all water that falls in the basin ends up in Devils Lake and stays there (minus evaporation and infiltration). Therefore, the wetlands in the Devils Lake basin would probably be of limited long-term value in preventing the rise of the lake. Pollution is another issue, however. Many farm chemicals would be neutralized in healthy wetlands within the Devils Lake basin, meaning there is still a very good environmental reason to restore them.
2) Geological evidence clearly indicates that Devils Lake has risen to its overspill level many times and has also completely dried up in geologically recent times (post Lake Agassiz, making a comparisons of Lake Agassiz to Devils Lake's changes moot). What the lake has gone through over the last few decades is all part of a natural cycle.