I think the problem was that the US did not have any "plans" what to do with the Aleuts  (or anyone else) before hand. 
If you read up on history, they (US) knew and had started military build up in Alaska prior to the bombing of Pearl Harbor. 
There was confusion and disconnect over who was "in charge" of which Aleuts. 
The "what to do" ended up happening quickly. No one and nothing was prepared.
A day or two before Pearl Harbor the area was put under control of the US military. 
By rounding up the Aleuts it certainly did "freed up land/areas" that were never returned after the war was over. 
Remember, the Aleuts may have had facial features similar to the Japanese, they also had facial features to the Chinese, (who were our allies), and who was at war with Japan.  
The "inter-marriage" between Aleuts and the Russians for over 150 years before caused some Aleuts to look and speak more "Russian".  Russians had been allies with us in WWI  and again later in WWII.