It is best to always avoid the application of negative inputs to chip like your microcontroller. The data sheets almost always show the -0.3v or -0.5v input limit in the ABSOLUTE MAXIMUM ratings section. Trying to design up to these limits is like playing 6 shooter roulette with your microcontroller. I would also suggest that you go with a design that runs with the chip inputs running between GND and V_IL while they are in the low state. If that takes a separate buffer transistor then so be it.

There are comparators that have a separate output stage Vss pin that permits you to have a ground referenced output whilest still having the input section of the chip able to operate at bipolar voltages above and below ground. You may want to look at this possibility. I seem to recall a part number like LM311.

There are also now some comparators on the market that will permit the comparison of voltages on the inputs that go below ground even though the Vss pin of the part is at ground. These are a good choice for interface to a microcontroller becasue the output is constrained to swing only to ground. Look at the LT1716 for example.

Michael Karas