Most of us have the same thoughts you do at some point or other about 'what if' when going on track with a nice bike. I take the view that I bought the bike to enjoy it, and the track is the best place for me to do that. I try to take a measured approach with an acceptable level of risk so I can relax and enjoy myself.
I do the bins BMW road bike only trackdays each year now, there are two or three a year. It's a nice way to get on track without worrying about some tw@t on something worthless being thrown at your pride and joy, as everyone pretty much needs to ride home after. Plus because everything has to be mot / roadworthy the standard of bikes is generally high, and also no tyre warmers/slicks keeps the Rossis away. I went to the inaugural NL road bike only day at Donnington recently and it was very good too. I think these are gaining in popularity.
I also do normal trackdays that I ride to, which puts me in a minority.
To offset the risk enough for me, I invested in crash protection and some disposable road fairings, ride in the fast groups (usually higher general standard of riders) and not really had any problems, not wishing to tempt fate.
The reality is that we will always have the possibility of crashing, but if that is your mindset then simply don't go. I have never seen a collision on track that led to a crash, your mate was very unfortunate IMO. The offs I have seen have usually been rider error, and occasionally vehicle malfunction. I have been to a couple of the bins BMW trackdays where there have been no red flags all day whatsoever.
One thing I can guarantee is that if you are not relaxed on your bike, it won't be a good experience and you won't have fun.