I think you should just make the change to the crystals you suggested. The fact that it allows a backroute with that builder glitch doesn't matter because (1) there is a backroute with that glitch already, and (2) combining that with the other glitch needed for the solution probably makes it harder than the real solution.
As for how to move the crystals, I would suggest moving the one crystal that touches the red line on the right to just miss the line, and then moving the entire block of crystals sufficently far left.