No expensive Gore-Tex jacket will degrade at a material level to the point where it needs structural reinforcement during a reasonable lifetime of a jacket. You'd need to regularly use the jacket improperly. Simply using a rucksack just won't do it.
The "degradation" you are referring to is caused by the DWR (durable water repellent) coat rubbing off. This is a hydrophobic chemical coating applied to the fabric that complements the Gore-Tex membrane to improve waterproofing and breathability. To simplify, the DWR makes the water ball up and fall off the jacket rather than soak in. Over time the DWR wears off and the water can begin to soak in (a phenomena often called "wetting out") making the jacket seem less waterproof.
There is not a lot you can do to prevent the DWR from wearing off. Anything you do to protect the coat is likely to just make the performance of the coat worse. You could try to add something to the bag that is lower friction but I think the benefit will be minimal. The standard practice is a reactive measure. You simply just reapply a DWR coat to your jacket. There are a number of brands that make DWR products. I personally (not affiliated) have used Nikwax products for years on many jackets and have had great success. Nikwax (along with most other brands) has two styles, a spray-on and a wash-in. The wash-in versions are generally superior and last longer. If you are just seeing the DWR come off on the shoulders though then the spray-on may make more sense for you to touch up the shoulder areas. Whatever brand you go with will have specific instructions for reapplying their DWR, but they are all pretty straightforward.
In short, when you see your jackets waterproofing degrading just reapply a DWR coat using any of the wash-in or spray-in products available.