I would like to add, that In this case the untrusted network is not open internet, and I am not running any encryption. So stateful encryption issues wont bother me here.
I was thinking, of changing some PPP option to tolerate and accept packets out of order, rather than buffering and waiting for the right one. I can not find such an option.
According to the RFC, some GRE loss could be tolerated by a decryptor provided that a higher layer stateful encryption is not used.
To be 100% clear, The packet loss is the GRE raw packets themself, not data inside the GRE tunnel.
The entire link fails and reconnects, resetting sequence to zero, and re negotiating.