MODE-1954 Corrected code that removes property definition during registration

The code that removes existing property definitions when storing a
node type template did not properly remove the node under
'/jcr:system/jcr:nodeTypes' that represented the property definition.
Instead, it merely removed it from its parent, but left the node
(which could not be found in its parent when later processed).
There was a bold node in the JavaDoc for the method stating this
behavior, so it was merely a method call that was not corrected a while
back.

The test case failed with the same exception, and now succeeds
with the aforementioned fix.