Moving countries isn't easy, and getting settled in a new location takes time.
The 5 year rule is part of the existing freedom of movement regulation. It provides additional protection against getting kicked out in case of sickness or unemployment.
Exercising the right to live and work anywhere in the EU before Brexit takes effect may well mean that you can keep those rights after Brexit and acquire permanent residence rights later on.
Anything else would mean that hundereds of thousands of people would have to be deported, which would go against every promise made in the referendum campaign.
From there you might have to wait N-years for citizenship, but freedom of movement hasn't been curtailed at the moment, even if it might be in the future.
The only potential spanner in the works is the question of what happens to foreigners in the UK, and the reciprocal agreement that has yet to be agreed. But it seems extraordinarily unlikely a UK-citizen who gained residency in German would be told to leave in two years time.
I'm not happy about the Brexit vote, but in all honesty even with the "Leave" result I don't think I'd have left the country.
(As it happens I left the year before, for unrelated reasons, but I'm a little glad I left.)