spring 3 autowiring and junit testing

I want to test in isolation class A.

You should absolutely mock B, rather than instantiate and inject an instance of B. The point is to test A whether or not B works, so you should not allow a potentially broken B interfere with the testing of A.

That said, I highly recommend Mockito. As mocking frameworks go, it is extremely easy to use. You would write something like the following:

@Test
public void testA() {
    A a = new A();
    B b = Mockito.mock(B.class); // create a mock of B
    Mockito.when(b.getMeaningOfLife()).thenReturn(42); // define mocked behavior of b
    ReflectionTestUtils.setField(a, "b", b); // inject b into the B attribute of A

    a.method();

    // call whatever asserts you need here
}