Until this is done, if at all, you could use AutoHotkey to convert plain keystrokes into their Ctrl counterpart.
http://ahkscript.org/

GnuBgKeys.ahk
;---------------------------------------
; If GnuBg's main window is the active window...
#IfWinActive ahk_class gdkWindowToplevel

; Take action on the following keystrokes:
d:: SendInput ^d  ;<D> sends <Ctrl-D> to double
a:: SendInput !ga ;<A> sends <Alt-G><A> (menu option) to accept
j:: SendInput !gj ;<J> sends <Alt-G><J> (menu option) to drop
r:: SendInput ^r  ;<R> sends <Ctrl-R> to roll the dice
f:: SendInput ^f  ;<F> sends <Ctrl-F> to pick up the dice

#IfWinActive
;---------------------------------------

You can change the keys before the '::' to suit yourself and add any other definitions that you like. For instance, you might prefer ::c for Cube (double), ::t for Take (accept), ::p for Pass (reject), ::d for Dice (roll), etc.

The keys that are sent must be what GnuBg is expecting. ^ repesents Ctrl, + is Shift and ! is Alt. Comments are denoted by ; and can be edited or removed without effect.