Although there are some rough sections between Iquique and Santiago most of the Panamericana is (comparatively) smooth and flat, although the last time I did this section parts of the road had gone due to an earthquake. I think you should be fine providing you top up regularly (keeping the levels in each fork the same) and take it VERY steady, particularly on the steep windy decents where much of your weight will be over the front (e.g. around Antofagasta). Are you sure there is no BMW dealer in Antofagasta or Copiapo? Probably not, but I wouldn't know for sure. The worst that can happen is that you'll end up with a dangerous pogo-like ride, and you can manage that if you take it steady. I have had this problem on an old Tenere, and it is possible to get used to it. I've heard this is common on F650GS's. Why did BMW not fit fork gaitors?? When you get this fixed it might be wise to invest in some.......
In short, I would risk it.
One other thought. I have no idea if it will work or not, but it might be possible to use some of that engine stop leak on the forks (Holts or similar if you can get it). It's bound to affect the fork oil viscosity, but it might just make the seals expand enough to get you to Santiago with minimum loss. It's helped me before.......
Tall men see everyone else's bald patch but their own.......