A program is non-free if you, the user, don't have the four freedoms. So
that's a simple question: of course deleting the source code would make it
non-free.
But I suppose the more interesting question is: is it *unethical*? That one's
a little more interesting because what's unethical about non-free software is
that a developer controls a user through that software. If the developer and
the user are the same person, and that one person discards the source code,
this person's freedom hasn't been violated by someone else; rather, this
person has decided to abandon the option to modify this program they wrote.
So my conclusion is it isn't unethical.
Another related question: would distribution of a non-free program whose
source code is no longer available to its developers to people who aren't
developers be unethical? Well, it's still perfectly possible for there to be
a backdoor or spyware in the program that the developers can take advantage
of, so it's impossible to tell for an individual program. If such malicious
features exist and the developers can take advantage of them, it's unethical;
otherwise, I think it isn't. But if the possibility of such malicious
features being there exists (i.e. the program runs on a computer with a
connection to the Internet), it has to be treated as something that the
developers could have some control over, since there's no way to find out if
they do or don't.