I think deprecating and un-recommending this option in the manual page will be a good start (and I just now noticed that https://savannah.gnu.org/bugs/?32501 asked for the same thing). I think that the only reason people use this variable is that they read through the manual page, and thought it would be cool to set it to something like "--with-color -n". So the manual page should be clear that it's not cool to use it, and what the alternative is.

I don't mind that people use such an option if they are well aware of what they are doing, and if they are aware that it is their environment which is broken, not the shell scripts they use, and don't expect every shell script which uses grep to begin with "unset GREP_OPTIONS".

Here is a patch I propose to the grep(1) manual page:

diff --git a/grep.1.orig b/grep.1
index fb99665..9d2a8d3 100644
--- a/grep.1.orig
+++ b/grep.1
@@ -875,6 +875,21 @@ had been specified before any explicit options.
 Option specifications are separated by whitespace.
 A backslash escapes the next character,
 so it can be used to specify an option containing whitespace or a backslash.
+
+This variable is deprecated, and should be avoided. Setting it changes not
+only the behavior of
+.B grep
+in interactive shell sessions, but may also break shell scripts and makefiles
+which assume that
+.B grep
+behaves normally. A user that wishes to alter the default
+.B grep
+behavior only for interactive sessions should instead use the
+.I alias
+feature provided by the shell, e.g.,
+.EX
+alias grep='grep --color=auto -n'
+.EE
 .TP
 .B GREP_COLOR
 This variable specifies the color used to highlight matched (non-empty) text.

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