Currently, the cookies set when logging in via the API are always persistent. It would be nice if ApiLogin.php took an optional boolean parameter to control this behavior and passed it along to LoginForm (via the wpRemember parameter).
This should be pretty easy to implement, I just don't feel like doing it just now and I'm not that familiar with the API internals anyway. I might do it sometime later if no-one else does it first.
Sort of related to bug 26538, but not really the same thing.