And then you have a possibly confusing situation where you have two programs that do essentially the same thing, but one is faster, and the other one is possibly not provided by default. As a user, in cases it matters, you'd have to know the issue and bother installing the new program. This is worse. As developers, I think it's our duty to make life of users simpler, even if it makes our lives a bit more complicated. I'd argue that's what we are here for.
I guess there's no ideal solution. But I think the "new" program does what the first one did better, and does not do anything worse.
We are talking about a program that still under 1000 lines of code and that's not getting new features every month, or at all anyway, so maintainability does not seem to be a big issue?
I see the reasoning but I don't see any actual practical drawback to have improved the original program directly in this specific case. I don't see any advantages of keeping "yes" dead simple neither. The new version is still pretty much readable and the extra time it takes to read it and modifying without doing mistakes seems worth the advantages.