I don't think that having many solutions is a problem for a programming game. The last one I played, Opus Magnum, had countless solutions for every level, and it was part of the appeal of that game. :-) I think the real problem would be implementing the programming game controls and mechanics in RPG Maker. From what I've seen in my time with it, it is not particularly flexible in regards to the interface unless you go really deep into scripting.