I was recently out of town and my AC was off, while I was away a tree next to my house was struck by lightning. When I came back into town my AC unit wouldn't function and I was informed I needed to replace the entire unit which was only 2 years old, does this seem accurate?

What exactly did they say was wrong with your unit ?

Who informed you of this? Was your unit examined by a HVAC professional?

But it certainly IS possible. Was anything else electrical or electronic damaged in your place?

Is it possible... yes. Is it likely that the entire system would be affected... no.
There may be a bright side... your insurance should cover the lightning strike.
But the burden of proof is on you. Call the insurance company and hand the ball to them.

I can tell you what happened to me. Lightning hit my mountain house. Blew all AFCI breakers, the control board, gas valve and thermostat on an Armstrong 92%. Insurance company estimate was $900. I have a $1000 deductible. I paid out of pocket $650 to repair the HVAC and replaced the breakers myself. Ended up at $800. Took a loss on Income Taxes. I would be surprised if a unit is totaled that way.