If you dont want to mark the ali cover the cut line with wide masking tape to protect the surface from the jigsaw skids. If you have some thin ply to waste plonk the ali on top of that and cut through both at the same time, that allows you to apply downward pressure to the jigsaw without deforming the ali sheet. If you are cutting long straight lines you can use a cheap hardpoint woodsaw providing you are using the wood underneath. Much better on the long cuts than a jigsaw.
Works for me
Bob