The knowledge gained from both tye and btrott's wisdom will surely benefit me in the future, but mirod's offering seems like the right thing to do in this case. I was so focused on the lists it didn't occur to me to go back to XML::Simple's documentation for a way to alter the list. Adding forcearray to XMLin() eliminates the problem.

my$data = XMLin($url, forcearray => 1);
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Results in the following for a single entry (note the [ and ], they're not present without forcearray):

$data = {
   'foo' => [{
             'one' => '1',
             'two' => '2'
            }]
  };
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Thank you all!

Update: I've found that sometimes you also must specify which hash to force by specifying the keyattr.

my$data = XMLin($url, keyattr => 'foo', forcearray => 1);
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