Go with a good independent specializing in European cars. You'll save money and get better service in most cases. Build a relationship with this independent so you can trust their advice on future repairs.
The cost of rotors is reasonable, so you might as well replace them now along with new pads. Today's rotors just don't have much additional metal to remove. If they can be turned one more time, you'll probably need to replace the rotors again while your existing pads are still good. Then you'l have mismatched pads and rotors.
Replace the rotors now and forget about them until the next brake job. My 2 cents worth.
2000 Lexus RX300