How to read “E = (mc)²” so as not to mistake for “E = mc²”

As a member of the mathematics community for many years, I'd say the standard pronunciation is:

E equals the quantity MC squared

Also, as pointed out by Mark Adler in the comments, this is the standard pronunciation used when recording mathematics textbooks for the blind (thanks for the info Mark!).

Trying to swap things around to make it the least ambiguous possible and still sound light:

E equals the square of MC

The word all can be used to indicate the grouping that is shown in print by brackets, so this could be read as

E equals M C all squared

In this specific example that’s probably sufficient for a listener to realise you’re saying something different from the more common “E equals M C squared”, and the correct meaning ought to be clear because it’s a simple expression with no other plausible interpretation – but in the general case it can be extremely difficult to express the precise meaning of an arbitrarily complex equation using a natural language in place of a symbolic one.