distroyed engine

Here is my saga that I have not been able to resolve on the sequoia forums. I took my 08 Toyota sequoia into the dealership for a new water pump. It has the 5.7 liter as in the Tundra and a timing chain not belt. The old Pump was barely dripping, just started, after 96000 miles.

The dealer gave me a loaner and the next day I called about pickup and was told that they were having a timing issue. The next day I called and the service tech said he thought it had a bearing issue. I went to look at the vehicle and the engine and transmission were out, the valve covers were off and they said they were pulling the pan. The next day I was told it threw a mainbearing but not to worry because since it was "on their watch" they would cover all costs.

The whole thing stinks of a major screwup and cover-up and I have a lot to consider. What stumps me is how a simple water pump change can go so wrong. Can someone help and explain how the water pump may be connected to the timing and bearing failure? I am desperate for some advise and understanding of what may have happened.