Hi All,
Before you read on, I want to be upfront and let you know that I don't have a solution....for you. I just wanted to throw my hat into the ring because I'm having these same problems and found your posts after doing a Google search. My issues are the same as yours, here they are:
1. I have the most recent rMBP15 that I just bought this past summer.
2. Everything was awesome until I installed El Cap.
3. Since then Safari crashes by either freezing itself, freezing the entire system (but the cursor still moves around), or rebooting itself by first displaying the black screen of death. This happens when:
a. I watch a Youtube video.
b. I open a new tab after watching a Youtube video, then closing the Youtube tab.
c. Once when I was simply viewing pictures on Flickr.
4. When Safari crashes and brings my system down with it (I thought Mac apps were sandboxed so that this didn't happen??), my SSD requires "fixing." So I have to boot to recovery mode and use First Aid to fix it.
So here's what I did first: disabled, then ultimately uninstalled all Safari extensions. Cleared the cache via developer menu. Reset Safari by erasing all website data including cookies and history. None of that worked. Recently after yet another crash, I reset Safari again then rebooted. Then I uninstalled Flash and rebooted. The last thing I did, which you won't like but seems to have made Safari stable again, I stopped using Youtube. Instead, when I want to watch Youtube videos I use my iPad. That's unacceptable considering I just paid $2,500 for this MacBook just a few months ago!!!!!!! But at least now Safari and my MacBook are usable again whereas beforehand I couldn't rely on it to do anything.
I have sent notes to Apple and also sent those reports (after a crash) with full details of what I was doing each time....probably sent over 15 of those at this point. No response. And the two dot updates of 10.11.1 and 10.11.2 haven't fixed this issue at all.
So while I apologize for not offering a solution, I just wanted to ensure that I jump in the ring with everyone else to show that more and more users are having this same problem. Thank you all for your posts - at least I know it's not just me. 🙂 Hopefully Apple takes notice and fixes it.