> Does patching software legally make it a fork?

I'm not aware of any legal definition of a fork (IANAL etc.). There
are derivatives of copyrighted material, which open source licenses
allow (if they don't they're not usually regarded as open source).
Your correspondent is right, you have a fork in that the source they
are using is no longer the upstream, it may be a trivial patch (and a
trivial fork), but they're making a point about the difficulty of
maintaining this in what is effectively a distro (many packages and
sources) and that upstream is the best place for patches. Exactly
where people draw the line in patches that haven't made it into
upstream will vary between projects (you'll find many Fedora srpms
that contain patches), if it's not a critical one for many people
(e.g. heartbleed) then I wouldn't be surprised if they wait for the
patch to come in from upstream rather than patch it in the build,
especially if one person is looking after hundreds of packages. In the
meantime there is absolutely nothing stopping you from applying a
patch locally.