At this point, I dont think that there is any single program available that can automate ISD.
What starts the confusion from my point is "automating instructional design". So what are we talking about here? The D of ADDIE or the entire process? Automating instructional system design means the whole thing to me, where as design is just that..the D. This might seem picky, but taxonomy and domains need definition or we end up with the current dilemma where curriculum cant even be defined???
Rather than trying to automate ISD or ID, I would suggest starting with job aids that can be adapted, developed, expanded and defined for a general process and then with algorithms to use more expanded ones for those who are inexperienced. It is still my contention that cookie cutter design will never be the best design. Using automation to collect and store data, track changes in development etc. are practical and automated tools can be helpful in design, but they are still limited by the user. Automating some content design and delivery ( moodle etc), testing is possible, but that brings up a whole other can of worms about using the testing tool for the first time for the learner, etc.
Here is a set of job aids based on the Rothwell/Kazanas book
on the first page. Click each link on the left for more job aids or go to the main aid page
Try expanding them into Moodle
(has authoring tools), Dokeos