I agree with Ralf that we need a solution for this.
I can be a multi-step solution.
But right now, most GNU distributions are not putting much effort in
the GnuPG installation and setup help. For example: With Debian squeeze
you cannot deinstall gpg1 because the dependencies would drag down other
software. Yes, this is partly a packaging problem with should be solved on
Debian's side (as well), but if we want GnuPG to be successful we need to offer
users and packagers best practice and clear recommendations.
My suggestions:
a) Make the suggestions more clear that gpg2 only should be recommened only in
almost all installations
b) offer some safety nets if there are both installed and gpgconf is used.