When a contractor proposes shimming a sliding glass door with 2x4s, you need to stop and think. While it might make the door look okay for a quick fix, wood blocking in a high-exposure area like that introduces several long term problems. You are essentially building a structural compromise on the exterior of a piece of aluminum and glass. The biggest worry isn't just the ugly wood, but how that material will hold up to thermal expansion and moisture over the next few seasons. A rigid wooden shim is going to expand and contract differently than the door frame itself, likely leading to gaps or seal failures quickly.
Before you agree to anything, make sure you document exactly where the misalignment is relative to the rough opening. If the frame is off, the proper fix is usally to adjust the rough opening itself, or get the contractor to order a frame that matches the actual rough measurement. If the door cannot fit, the contractor is responsible for that waste and the cost of a correctly sized replacement. Don't just accept a makeshift solution. Since you've alredy paid half, keep detailed logs of every conversation and any measurements taken by anyone involved. That documentation is your leverage. If they can't deliver a product that fits correctly based on thier own measurements, they are responsible for the cost of making it work properly, which usually means a full replacement of the unit.