A few things I'm fearful of:
Lack of staff (most Brits don't want to work in food factories, let's face it)
Impact on our image in the world
Potential export tariffs or restrictions
How food safety legislation will change (or will we have to accept EU rules without a seat at the table?)
Some of our staff are nervous about it all, we may lose some 
Hi GMO, for what its worth my opinion.
I don't think any EU citizens currently working in the UK will be sent home and I can see that there will be a level of inward migration from the EU continuing. Maybe we can increase the minimum wage to a living wage that may motivate some of our unemployed to see employment as a worthwhile pursuit and get off benefits. Tariffs are possible, but we do a lot of importing from the EU and I'm sure any deal will aim to mitigate this. I don't see food safety legislation changing in the short term and we'll probably continue as we are.
It is a big unknown and very early day's, but change is never easy or without risk.
We are each currently in this process somewhere.
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From the sounds of it the politicians are beginning to accept it and now the long hard job of realizing it commences.
Regards,
Simon