It wouldn't necessarily change anything. Even if the UK leaves the EU, they would still have a trade agreement like Switzerland, Iceland and Norway have today via the EFTA. All three these countries are not EU member but are EASA member.
As far as labour goes, I think the UK has enough problems finding pilots for their aircraft. And if you fly for BA, Easy etc, you can have an EU base and still fly on an UK AOC. There are plenty Emirate pilots with AMS, FRA, LHR base that fly on an Emirate AOC.