If the strongest point in the system (subframe) was damaged like that, I'm not sure what you could do to keep that from happening again. Any top rack frame is going to do the same thing as long as you keep the same load on the system. The frame has a breaking point, which you exceeded. So if you want to keep loading the system the same way, you'll have to figure out a way to make the subframe stronger.
IMHO you need to spread the load out. Add some side bags? I know that is not the answer you might be looking for. I used to just have a top rack and didn't want the bulk of side bags. Now I have side bags and no top case and I have to say that I like it better.
Keep us posted if you are able to get the frame repaired.
2011 Versys 650
Even a fool is thought wise if he keeps silent... Proverbs 17:28