The array way seems to be the right way of doing it. see here.
If you insist on iterating through your original object, you can change your HTML to something like:
<li ng-repeat="(k,v) in entries">
{{k}} is {{v}}
<input type="text" ng-model="$parent.entries[k]"></input>
</li>
$parent
is used since ng-repeat
creates a child scope for each instance of the repeated element.