looks like guile automatically detects & links against readline. should be listed in its dependency and use flags (if possible).
Created attachment 337842 [details, diff] Patch enabling --with-readline and --without-readline for guile-1.8.8 Here you are :-) I pushed this to the lisp overlay, see the following link for ebuild changes http://git.overlays.gentoo.org/gitweb/?p=proj/lisp.git;a=commitdiff;h=d3860a29c593a0e03ee64c5b3a8407532f9006ce
I went with something a little different. Fixed in 1.8.8-r2.