There is, of course, a much more worrying interpretation of the phrase boys will be boys:

I (or someone I love/honour/cherish) did that (or something very like it) when I I (they) were young; therefore it can't be that bad.
This is essentially cultural inertia at work. An older generation are bending the rules because the rules were different (or appear to be different) when they were that age. The real problem is when certain portions of the younger generation take on the mantle of the bent rules rather than the `real' rules.