How can I do A/D conversion with isolation?
There are a few ways to do this.

1) Convert to a digital signal and isolate that. You'd need an A/D converter of some kind on the signal-side of your isolation barrier. I've done this with CANbus and a full-scale microprocessor on the signal side, but that may be overkill for your purposes. I've also done it with SPI, which all ATMEGA 32 models I see have, and a stand-alone A/D converter. I used Microchip MCP3004, but Digikey lists hundreds that may work for you.

2) Use an analog optocoupler, like HCNR200 or LOC110. They require some external op-amps to run properly, so it's got a sizable footprint per signal. We found that the HCNR200 line held its linearity much better with temperature than the LOC110 did.

3) Use an isolation amplifier. I've only ever used the HCPL-7800, which gives output centered at 2.5V. That makes it problematic for DC purposes, but for AC it's quite nice. I couldn't comment on other varieties that might be out there.

4) Convert the analog signal to a PWM signal, and isolate that with a digital opto. I did this once, but then the fever broke. It's probably not worth the trouble given the other options.

My suggestion would be 1) or 2), depending on constraints like footprint, power consumption, and parts cost.