Changes have been made in Git for this ticket:

[jan] Add -N parameter to mailbot calls by default (Request #10147).

  4 files changed, 9 insertions(+), 1 deletions(-)
http://git.horde.org/horde-git/-/commit/8551ffaa1eec7c6a92a12d8f17c51900b09d650d

and for those who are only using maildrop, not the whole courier 
mail/groupware, this has been changed in version maildrop-2.5.1

http://www.courier-mta.org/maildrop/changelog.html :
2010-08-15  Sam Varshavchik  <mrsam@courier-mta.com>
        * rfc2045/rfc2045reply.c: added donotquote option, to suppress 
autoreply text.
        * maildrop/mailbot.c (main): Add the -N option to mailbot, to set the 
donotquote option.
        * maildir/maildirfilter.c: "noquote" autoreply option adds the -N 
option to the mailbot command line.

See also http://markmail.org/thread/6pf73ylv4hsufdjr
According to http://www.courier-mta.org/changelog.html, the -N flag 
has been added with 0.65.1, I don't see anything in the changelog when 
the quoting has been enabled, but according to the mailing list thread 
between 0.63 and 0.65.

It looks like it.
You can't. I seen two options here :
- apply the previous patch in git and add a maildrop version 
requirement in docs (and test.php ?)
- add a command line option in backend.[local].php. in case of 
maildrop, something like
$backends['maildrop']['scriptparams']['args'] = " -N "

and patch will then looks like this:

--- ingo/lib/Script/Maildrop/Recipe.php.org        2011-05-27
14:02:35.000000000 +0200
+++ ingo/lib/Script/Maildrop/Recipe.php        2011-05-27 
14:02:41.000000000 +0200
@@ -153,1 +153,1 @@
-   '| mailbot -D %d -c \'UTF-8\' -t $HOME/vacation.msg -d 
$HOME/vacation -A %s -s %s /usr/sbin/sendmail -t',
+  '| mailbot ' . $backends['maildrop']['scriptparams']['args'] . ' -D 
%d -c \'UTF-8\' -t $HOME/vacation.msg -d $HOME/vacation -A %s -s %s 
/usr/sbin/sendmail -t',

The second option is much more flexible and can apply to other drivers 
like procmail.
It will be up to the admin to tune is backend.local.php.

This sounds like a BC breaking change in mailbot. How are we supposed 
to know which version is running on that system?

It's rather old (August 2010), but after updating the maildrop package 
today, I noticed that mailbot's default behaviour has changed.

Fom the man page : "
-N
Do not quote the contents of the original message in the message 
create by ?reply?, ?replyall?, and ?replydsn? options. The original 
message gets quoted, in the absence of this option, only if the 
original message was formatted as plain text. mailbot is unable to 
quote an original message which was formatted as HTML, or any other 
non-plaintext format.
"

So here is a patch to mimic the old behaviour (what an end user would 
expect) of the vacation rule,

--- ingo/lib/Script/Maildrop/Recipe.php.org        2011-05-27 
14:02:35.000000000 +0200
+++ ingo/lib/Script/Maildrop/Recipe.php        2011-05-27 14:02:41.000000000 +0200
@@ -153,1 +153,1 @@
-   '| mailbot -D %d -c \'UTF-8\' -t $HOME/vacation.msg -d 
$HOME/vacation -A %s -s %s /usr/sbin/sendmail -t',
+  '| mailbot -N -D %d -c \'UTF-8\' -t $HOME/vacation.msg -d 
$HOME/vacation -A %s -s %s /usr/sbin/sendmail -t',