Actually I've found in researching my own school list that the 2 science instructor, plus 1 non-science instructor rule is the very small minority. A lot of schools are just looking for people that can judge your academic aptitude, and so have requirements like:
"2 from people knowledgeable about your scientific aptitude (PIs or academic mentors count)"
"2 from instructors of upper-division courses (science or non-science)"
"3 from teachers at your undergrad (science or non-science)"
"1 from science faculty"
"2 from courses, at least one of which is science"
Quite a few have no specific requirements at all. In the rare case one might be required from a non-academic individual (e.g. a volunteer or work supervisor). It depends entirely on what schools you're applying to. And if you're missing one of the 'holy trinity', there are still tons of schools you will be able to apply to with what letters you have. I wasn't sure if I was going to be able to get a second science instructor letter this year, but even if I hadn't I would only have had to replace 2 schools off my list of 20. And since the second science letter I got is from someone who hasn't known me as long as the rest of my letters, that one will only be going to the schools that specifically require it.
The 2 science, one non-science instructors rule is good because you will be able to apply to almost any school with those three letters. But 1 science, 1 non-science, and 1 flexible (science/non-science/research as you have available) still seems to qualify you for 90% of schools.