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The answer is NO. We had the same problem with the AT90CAN128.
Initially we just had both JTAG and the analog signals connected and this blew pins on the micro after some time (days).
Then we placed 10k series resistors between the micro and the analog sources with the JTAG connected directly to the processor. This works, but as long as your JTAG is connected, you can't actually use the analog inputs. There are some ways to get it to work with JTAG connected but inactive, but the voltage levels are influenced by the JTAG.
At least using the 10k resistors, you can use JTAG for programming and some testing, and then disconnect to use the analog inputs -- without causing damage.